forked from lijiext/lammps
1265 lines
62 KiB
HTML
1265 lines
62 KiB
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<title>10. Modifying & extending LAMMPS — LAMMPS documentation</title>
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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_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 current"><a class="current reference internal" href="#">10. Modifying & extending LAMMPS</a><ul>
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<li class="toctree-l2"><a class="reference internal" href="#atom-styles">10.1. Atom styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#bond-angle-dihedral-improper-potentials">10.2. Bond, angle, dihedral, improper potentials</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#compute-styles">10.3. Compute styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#dump-styles">10.4. Dump styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#dump-custom-output-options">10.5. Dump custom output options</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#fix-styles">10.6. Fix styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#input-script-commands">10.7. Input script commands</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#kspace-computations">10.8. Kspace computations</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#minimization-styles">10.9. Minimization styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#pairwise-potentials">10.10. Pairwise potentials</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#region-styles">10.11. Region styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#body-styles">10.12. Body styles</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#thermodynamic-output-options">10.13. Thermodynamic output options</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#variable-options">10.14. Variable options</a></li>
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<li class="toctree-l2"><a class="reference internal" href="#submitting-new-features-for-inclusion-in-lammps">10.15. Submitting new features for inclusion in LAMMPS</a></li>
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</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>10. Modifying & extending LAMMPS</li>
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<a href="Section_commands.html#comm">Commands</a>
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<div class="section" id="modifying-extending-lammps">
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<h1>10. Modifying & extending LAMMPS</h1>
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<p>This section describes how to customize LAMMPS by modifying
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and extending its source code.</p>
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<div class="line-block">
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<div class="line">10.1 <a class="reference internal" href="#mod-1"><span class="std std-ref">Atom styles</span></a></div>
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<div class="line">10.2 <a class="reference internal" href="#mod-2"><span class="std std-ref">Bond, angle, dihedral, improper potentials</span></a></div>
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<div class="line">10.3 <a class="reference internal" href="#mod-3"><span class="std std-ref">Compute styles</span></a></div>
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<div class="line">10.4 <a class="reference internal" href="#mod-4"><span class="std std-ref">Dump styles</span></a></div>
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<div class="line">10.5 <a class="reference internal" href="#mod-5"><span class="std std-ref">Dump custom output options</span></a></div>
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<div class="line">10.6 <a class="reference internal" href="#mod-6"><span class="std std-ref">Fix styles</span></a> which include integrators, temperature and pressure control, force constraints, boundary conditions, diagnostic output, etc</div>
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<div class="line">10.7 <a class="reference internal" href="#mod-7"><span class="std std-ref">Input script commands</span></a></div>
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<div class="line">10.8 <a class="reference internal" href="#mod-8"><span class="std std-ref">Kspace computations</span></a></div>
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<div class="line">10.9 <a class="reference internal" href="#mod-9"><span class="std std-ref">Minimization styles</span></a></div>
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<div class="line">10.10 <a class="reference internal" href="#mod-10"><span class="std std-ref">Pairwise potentials</span></a></div>
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<div class="line">10.11 <a class="reference internal" href="#mod-11"><span class="std std-ref">Region styles</span></a></div>
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<div class="line">10.12 <a class="reference internal" href="#mod-12"><span class="std std-ref">Body styles</span></a></div>
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<div class="line">10.13 <a class="reference internal" href="#mod-13"><span class="std std-ref">Thermodynamic output options</span></a></div>
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<div class="line">10.14 <a class="reference internal" href="#mod-14"><span class="std std-ref">Variable options</span></a></div>
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<div class="line">10.15 <a class="reference internal" href="#mod-15"><span class="std std-ref">Submitting new features for inclusion in LAMMPS</span></a></div>
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<div class="line"><br /></div>
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</div>
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<p>LAMMPS is designed in a modular fashion so as to be easy to modify and
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extend with new functionality. In fact, about 75% of its source code
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is files added in this fashion.</p>
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<p>In this section, changes and additions users can make are listed along
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with minimal instructions. If you add a new feature to LAMMPS and
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think it will be of interest to general users, we encourage you to
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submit it to the developers for inclusion in the released version of
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LAMMPS. Information about how to do this is provided
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<a class="reference internal" href="#mod-14"><span class="std std-ref">below</span></a>.</p>
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<p>The best way to add a new feature is to find a similar feature in
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LAMMPS and look at the corresponding source and header files to figure
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out what it does. You will need some knowledge of C++ to be able to
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understand the hi-level structure of LAMMPS and its class
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organization, but functions (class methods) that do actual
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computations are written in vanilla C-style code and operate on simple
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C-style data structures (vectors and arrays).</p>
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<p>Most of the new features described in this section require you to
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write a new C++ derived class (except for exceptions described below,
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where you can make small edits to existing files). Creating a new
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class requires 2 files, a source code file (<em>.cpp) and a header file
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(</em>.h). The derived class must provide certain methods to work as a
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new option. Depending on how different your new feature is compared
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to existing features, you can either derive from the base class
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itself, or from a derived class that already exists. Enabling LAMMPS
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to invoke the new class is as simple as putting the two source
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files in the src dir and re-building LAMMPS.</p>
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<p>The advantage of C++ and its object-orientation is that all the code
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and variables needed to define the new feature are in the 2 files you
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write, and thus shouldn’t make the rest of LAMMPS more complex or
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cause side-effect bugs.</p>
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<p>Here is a concrete example. Suppose you write 2 files pair_foo.cpp
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and pair_foo.h that define a new class PairFoo that computes pairwise
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potentials described in the classic 1997 <a class="reference internal" href="#foo"><span class="std std-ref">paper</span></a> by Foo, et al.
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If you wish to invoke those potentials in a LAMMPS input script with a
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command like</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">foo</span> <span class="mf">0.1</span> <span class="mf">3.5</span>
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</pre></div>
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</div>
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<p>then your pair_foo.h file should be structured as follows:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1">#ifdef PAIR_CLASS</span>
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<span class="n">PairStyle</span><span class="p">(</span><span class="n">foo</span><span class="p">,</span><span class="n">PairFoo</span><span class="p">)</span>
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<span class="c1">#else</span>
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<span class="o">...</span>
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<span class="p">(</span><span class="k">class</span> <span class="nc">definition</span> <span class="k">for</span> <span class="n">PairFoo</span><span class="p">)</span>
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<span class="o">...</span>
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<span class="c1">#endif</span>
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</pre></div>
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</div>
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<p>where “foo” is the style keyword in the pair_style command, and
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PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h
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files.</p>
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<p>When you re-build LAMMPS, your new pairwise potential becomes part of
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the executable and can be invoked with a pair_style command like the
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example above. Arguments like 0.1 and 3.5 can be defined and
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processed by your new class.</p>
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<p>As illustrated by this pairwise example, many kinds of options are
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referred to in the LAMMPS documentation as the “style” of a particular
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command.</p>
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<p>The instructions below give the header file for the base class that
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these styles are derived from. Public variables in that file are ones
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used and set by the derived classes which are also used by the base
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class. Sometimes they are also used by the rest of LAMMPS. Virtual
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functions in the base class header file which are set = 0 are ones you
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must define in your new derived class to give it the functionality
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LAMMPS expects. Virtual functions that are not set to 0 are functions
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you can optionally define.</p>
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<p>Additionally, new output options can be added directly to the
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thermo.cpp, dump_custom.cpp, and variable.cpp files as explained
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below.</p>
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<p>Here are additional guidelines for modifying LAMMPS and adding new
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functionality:</p>
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<ul class="simple">
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<li>Think about whether what you want to do would be better as a pre- or
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post-processing step. Many computations are more easily and more
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quickly done that way.</li>
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<li>Don’t do anything within the timestepping of a run that isn’t
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parallel. E.g. don’t accumulate a bunch of data on a single processor
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and analyze it. You run the risk of seriously degrading the parallel
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efficiency.</li>
|
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<li>If your new feature reads arguments or writes output, make sure you
|
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follow the unit conventions discussed by the <a class="reference internal" href="units.html"><span class="doc">units</span></a>
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command.</li>
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<li>If you add something you think is truly useful and doesn’t impact
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LAMMPS performance when it isn’t used, send an email to the
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<a class="reference external" href="http://lammps.sandia.gov/authors.html">developers</a>. We might be
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interested in adding it to the LAMMPS distribution. See further
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details on this at the bottom of this page.</li>
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</ul>
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<div class="section" id="atom-styles">
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<span id="mod-1"></span><h2>10.1. Atom styles</h2>
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<p>Classes that define an <a class="reference internal" href="atom_style.html"><span class="doc">atom style</span></a> are derived from
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the AtomVec class and managed by the Atom class. The atom style
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determines what attributes are associated with an atom. A new atom
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style can be created if one of the existing atom styles does not
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define all the attributes you need to store and communicate with
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atoms.</p>
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<p>Atom_vec_atomic.cpp is a simple example of an atom style.</p>
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<p>Here is a brief description of methods you define in your new derived
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class. See atom_vec.h for details.</p>
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<table border="1" class="docutils">
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<colgroup>
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<col width="22%" />
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<col width="78%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td>init</td>
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<td>one time setup (optional)</td>
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</tr>
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<tr class="row-even"><td>grow</td>
|
||
|
|
<td>re-allocate atom arrays to longer lengths (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>grow_reset</td>
|
||
|
|
<td>make array pointers in Atom and AtomVec classes consistent (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>copy</td>
|
||
|
|
<td>copy info for one atom to another atom’s array locations (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pack_comm</td>
|
||
|
|
<td>store an atom’s info in a buffer communicated every timestep (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>pack_comm_vel</td>
|
||
|
|
<td>add velocity info to communication buffer (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pack_comm_hybrid</td>
|
||
|
|
<td>store extra info unique to this atom style (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>unpack_comm</td>
|
||
|
|
<td>retrieve an atom’s info from the buffer (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>unpack_comm_vel</td>
|
||
|
|
<td>also retrieve velocity info (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>unpack_comm_hybrid</td>
|
||
|
|
<td>retreive extra info unique to this atom style (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pack_reverse</td>
|
||
|
|
<td>store an atom’s info in a buffer communicating partial forces (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>pack_reverse_hybrid</td>
|
||
|
|
<td>store extra info unique to this atom style (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>unpack_reverse</td>
|
||
|
|
<td>retrieve an atom’s info from the buffer (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>unpack_reverse_hybrid</td>
|
||
|
|
<td>retreive extra info unique to this atom style (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pack_border</td>
|
||
|
|
<td>store an atom’s info in a buffer communicated on neighbor re-builds (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>pack_border_vel</td>
|
||
|
|
<td>add velocity info to buffer (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pack_border_hybrid</td>
|
||
|
|
<td>store extra info unique to this atom style (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>unpack_border</td>
|
||
|
|
<td>retrieve an atom’s info from the buffer (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>unpack_border_vel</td>
|
||
|
|
<td>also retrieve velocity info (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>unpack_border_hybrid</td>
|
||
|
|
<td>retreive extra info unique to this atom style (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pack_exchange</td>
|
||
|
|
<td>store all an atom’s info to migrate to another processor (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>unpack_exchange</td>
|
||
|
|
<td>retrieve an atom’s info from the buffer (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>size_restart</td>
|
||
|
|
<td>number of restart quantities associated with proc’s atoms (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>pack_restart</td>
|
||
|
|
<td>pack atom quantities into a buffer (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>unpack_restart</td>
|
||
|
|
<td>unpack atom quantities from a buffer (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>create_atom</td>
|
||
|
|
<td>create an individual atom of this style (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>data_atom</td>
|
||
|
|
<td>parse an atom line from the data file (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>data_atom_hybrid</td>
|
||
|
|
<td>parse additional atom info unique to this atom style (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>data_vel</td>
|
||
|
|
<td>parse one line of velocity information from data file (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>data_vel_hybrid</td>
|
||
|
|
<td>parse additional velocity data unique to this atom style (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>memory_usage</td>
|
||
|
|
<td>tally memory allocated by atom arrays (required)</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
<p>The constructor of the derived class sets values for several variables
|
||
|
|
that you must set when defining a new atom style, which are documented
|
||
|
|
in atom_vec.h. New atom arrays are defined in atom.cpp. Search for
|
||
|
|
the word “customize” and you will find locations you will need to
|
||
|
|
modify.</p>
|
||
|
|
<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>New <a class="reference internal" href="pair_style.html"><span class="doc">pair styles</span></a>, <a class="reference internal" href="fix.html"><span class="doc">fixes</span></a>, or
|
||
|
|
<a class="reference internal" href="compute.html"><span class="doc">computes</span></a> can be added to LAMMPS, as discussed below.
|
||
|
|
The code for these classes can use the per-atom properties defined by
|
||
|
|
fix property/atom. The Atom class has a find_custom() method that is
|
||
|
|
useful in this context:</p>
|
||
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">int</span> <span class="n">index</span> <span class="o">=</span> <span class="n">atom</span><span class="o">-></span><span class="n">find_custom</span><span class="p">(</span><span class="n">char</span> <span class="o">*</span><span class="n">name</span><span class="p">,</span> <span class="nb">int</span> <span class="o">&</span><span class="n">flag</span><span class="p">);</span>
|
||
|
|
</pre></div>
|
||
|
|
</div>
|
||
|
|
<p>The “name” of a custom attribute, as specified in the <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> command, is checked to verify
|
||
|
|
that it exists and its index is returned. The method also sets flag =
|
||
|
|
0/1 depending on whether it is an integer or floating-point attribute.
|
||
|
|
The vector of values associated with the attribute can then be
|
||
|
|
accessed using the returned index as</p>
|
||
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">int</span> <span class="o">*</span><span class="n">ivector</span> <span class="o">=</span> <span class="n">atom</span><span class="o">-></span><span class="n">ivector</span><span class="p">[</span><span class="n">index</span><span class="p">];</span>
|
||
|
|
<span class="n">double</span> <span class="o">*</span><span class="n">dvector</span> <span class="o">=</span> <span class="n">atom</span><span class="o">-></span><span class="n">dvector</span><span class="p">[</span><span class="n">index</span><span class="p">];</span>
|
||
|
|
</pre></div>
|
||
|
|
</div>
|
||
|
|
<p>Ivector or dvector are vectors of length Nlocal = # of owned atoms,
|
||
|
|
which store the attributes of individual atoms.</p>
|
||
|
|
<hr class="docutils" />
|
||
|
|
</div>
|
||
|
|
<div class="section" id="bond-angle-dihedral-improper-potentials">
|
||
|
|
<span id="mod-2"></span><h2>10.2. Bond, angle, dihedral, improper potentials</h2>
|
||
|
|
<p>Classes that compute molecular interactions are derived from the Bond,
|
||
|
|
Angle, Dihedral, and Improper classes. New styles can be created to
|
||
|
|
add new potentials to LAMMPS.</p>
|
||
|
|
<p>Bond_harmonic.cpp is the simplest example of a bond style. Ditto for
|
||
|
|
the harmonic forms of the angle, dihedral, and improper style
|
||
|
|
commands.</p>
|
||
|
|
<p>Here is a brief description of common methods you define in your
|
||
|
|
new derived class. See bond.h, angle.h, dihedral.h, and improper.h
|
||
|
|
for details and specific additional methods.</p>
|
||
|
|
<table border="1" class="docutils">
|
||
|
|
<colgroup>
|
||
|
|
<col width="23%" />
|
||
|
|
<col width="77%" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody valign="top">
|
||
|
|
<tr class="row-odd"><td>init</td>
|
||
|
|
<td>check if all coefficients are set, calls <em>init_style</em> (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>init_style</td>
|
||
|
|
<td>check if style specific conditions are met (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>compute</td>
|
||
|
|
<td>compute the molecular interactions (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>settings</td>
|
||
|
|
<td>apply global settings for all types (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>coeff</td>
|
||
|
|
<td>set coefficients for one type (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>equilibrium_distance</td>
|
||
|
|
<td>length of bond, used by SHAKE (required, bond only)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>equilibrium_angle</td>
|
||
|
|
<td>opening of angle, used by SHAKE (required, angle only)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>write & read_restart</td>
|
||
|
|
<td>writes/reads coeffs to restart files (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>single</td>
|
||
|
|
<td>force and energy of a single bond or angle (required, bond or angle only)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>memory_usage</td>
|
||
|
|
<td>tally memory allocated by the style (optional)</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
<hr class="docutils" />
|
||
|
|
</div>
|
||
|
|
<div class="section" id="compute-styles">
|
||
|
|
<span id="mod-3"></span><h2>10.3. Compute styles</h2>
|
||
|
|
<p>Classes that compute scalar and vector quantities like temperature
|
||
|
|
and the pressure tensor, as well as classes that compute per-atom
|
||
|
|
quantities like kinetic energy and the centro-symmetry parameter
|
||
|
|
are derived from the Compute class. New styles can be created
|
||
|
|
to add new calculations to LAMMPS.</p>
|
||
|
|
<p>Compute_temp.cpp is a simple example of computing a scalar
|
||
|
|
temperature. Compute_ke_atom.cpp is a simple example of computing
|
||
|
|
per-atom kinetic energy.</p>
|
||
|
|
<p>Here is a brief description of methods you define in your new derived
|
||
|
|
class. See compute.h for details.</p>
|
||
|
|
<table border="1" class="docutils">
|
||
|
|
<colgroup>
|
||
|
|
<col width="24%" />
|
||
|
|
<col width="76%" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody valign="top">
|
||
|
|
<tr class="row-odd"><td>init</td>
|
||
|
|
<td>perform one time setup (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>init_list</td>
|
||
|
|
<td>neighbor list setup, if needed (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>compute_scalar</td>
|
||
|
|
<td>compute a scalar quantity (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>compute_vector</td>
|
||
|
|
<td>compute a vector of quantities (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>compute_peratom</td>
|
||
|
|
<td>compute one or more quantities per atom (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>compute_local</td>
|
||
|
|
<td>compute one or more quantities per processor (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pack_comm</td>
|
||
|
|
<td>pack a buffer with items to communicate (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>unpack_comm</td>
|
||
|
|
<td>unpack the buffer (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pack_reverse</td>
|
||
|
|
<td>pack a buffer with items to reverse communicate (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>unpack_reverse</td>
|
||
|
|
<td>unpack the buffer (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>remove_bias</td>
|
||
|
|
<td>remove velocity bias from one atom (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>remove_bias_all</td>
|
||
|
|
<td>remove velocity bias from all atoms in group (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>restore_bias</td>
|
||
|
|
<td>restore velocity bias for one atom after remove_bias (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>restore_bias_all</td>
|
||
|
|
<td>same as before, but for all atoms in group (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pair_tally_callback</td>
|
||
|
|
<td>callback function for <em>tally</em>-style computes (optional).</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>memory_usage</td>
|
||
|
|
<td>tally memory usage (optional)</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
<p>Tally-style computes are a special case, as their computation is done
|
||
|
|
in two stages: the callback function is registered with the pair style
|
||
|
|
and then called from the Pair::ev_tally() function, which is called for
|
||
|
|
each pair after force and energy has been computed for this pair. Then
|
||
|
|
the tallied values are retrieved with the standard compute_scalar or
|
||
|
|
compute_vector or compute_peratom methods. The USER-TALLY package
|
||
|
|
provides <em>examples</em>_compute_tally.html for utilizing this mechanism.</p>
|
||
|
|
<hr class="docutils" />
|
||
|
|
</div>
|
||
|
|
<div class="section" id="dump-styles">
|
||
|
|
<span id="mod-4"></span><h2>10.4. Dump styles</h2>
|
||
|
|
</div>
|
||
|
|
<div class="section" id="dump-custom-output-options">
|
||
|
|
<span id="mod-5"></span><h2>10.5. Dump custom output options</h2>
|
||
|
|
<p>Classes that dump per-atom info to files are derived from the Dump
|
||
|
|
class. To dump new quantities or in a new format, a new derived dump
|
||
|
|
class can be added, but it is typically simpler to modify the
|
||
|
|
DumpCustom class contained in the dump_custom.cpp file.</p>
|
||
|
|
<p>Dump_atom.cpp is a simple example of a derived dump class.</p>
|
||
|
|
<p>Here is a brief description of methods you define in your new derived
|
||
|
|
class. See dump.h for details.</p>
|
||
|
|
<table border="1" class="docutils">
|
||
|
|
<colgroup>
|
||
|
|
<col width="22%" />
|
||
|
|
<col width="78%" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody valign="top">
|
||
|
|
<tr class="row-odd"><td>write_header</td>
|
||
|
|
<td>write the header section of a snapshot of atoms</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>count</td>
|
||
|
|
<td>count the number of lines a processor will output</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pack</td>
|
||
|
|
<td>pack a proc’s output data into a buffer</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>write_data</td>
|
||
|
|
<td>write a proc’s data to a file</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
<p>See the <a class="reference internal" href="dump.html"><span class="doc">dump</span></a> command and its <em>custom</em> style for a list of
|
||
|
|
keywords for atom information that can already be dumped by
|
||
|
|
DumpCustom. It includes options to dump per-atom info from Compute
|
||
|
|
classes, so adding a new derived Compute class is one way to calculate
|
||
|
|
new quantities to dump.</p>
|
||
|
|
<p>Alternatively, you can add new keywords to the dump custom command.
|
||
|
|
Search for the word “customize” in dump_custom.cpp to see the
|
||
|
|
half-dozen or so locations where code will need to be added.</p>
|
||
|
|
<hr class="docutils" />
|
||
|
|
</div>
|
||
|
|
<div class="section" id="fix-styles">
|
||
|
|
<span id="mod-6"></span><h2>10.6. Fix styles</h2>
|
||
|
|
<p>In LAMMPS, a “fix” is any operation that is computed during
|
||
|
|
timestepping that alters some property of the system. Essentially
|
||
|
|
everything that happens during a simulation besides force computation,
|
||
|
|
neighbor list construction, and output, is a “fix”. This includes
|
||
|
|
time integration (update of coordinates and velocities), force
|
||
|
|
constraints or boundary conditions (SHAKE or walls), and diagnostics
|
||
|
|
(compute a diffusion coefficient). New styles can be created to add
|
||
|
|
new options to LAMMPS.</p>
|
||
|
|
<p>Fix_setforce.cpp is a simple example of setting forces on atoms to
|
||
|
|
prescribed values. There are dozens of fix options already in LAMMPS;
|
||
|
|
choose one as a template that is similar to what you want to
|
||
|
|
implement.</p>
|
||
|
|
<p>Here is a brief description of methods you can define in your new
|
||
|
|
derived class. See fix.h for details.</p>
|
||
|
|
<table border="1" class="docutils">
|
||
|
|
<colgroup>
|
||
|
|
<col width="22%" />
|
||
|
|
<col width="78%" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody valign="top">
|
||
|
|
<tr class="row-odd"><td>setmask</td>
|
||
|
|
<td>determines when the fix is called during the timestep (required)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>init</td>
|
||
|
|
<td>initialization before a run (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>setup_pre_exchange</td>
|
||
|
|
<td>called before atom exchange in setup (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>setup_pre_force</td>
|
||
|
|
<td>called before force computation in setup (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>setup</td>
|
||
|
|
<td>called immediately before the 1st timestep and after forces are computed (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>min_setup_pre_force</td>
|
||
|
|
<td>like setup_pre_force, but for minimizations instead of MD runs (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>min_setup</td>
|
||
|
|
<td>like setup, but for minimizations instead of MD runs (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>initial_integrate</td>
|
||
|
|
<td>called at very beginning of each timestep (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pre_exchange</td>
|
||
|
|
<td>called before atom exchange on re-neighboring steps (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>pre_neighbor</td>
|
||
|
|
<td>called before neighbor list build (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pre_force</td>
|
||
|
|
<td>called before pair & molecular forces are computed (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>post_force</td>
|
||
|
|
<td>called after pair & molecular forces are computed and communicated (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>final_integrate</td>
|
||
|
|
<td>called at end of each timestep (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>end_of_step</td>
|
||
|
|
<td>called at very end of timestep (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>write_restart</td>
|
||
|
|
<td>dumps fix info to restart file (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>restart</td>
|
||
|
|
<td>uses info from restart file to re-initialize the fix (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>grow_arrays</td>
|
||
|
|
<td>allocate memory for atom-based arrays used by fix (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>copy_arrays</td>
|
||
|
|
<td>copy atom info when an atom migrates to a new processor (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pack_exchange</td>
|
||
|
|
<td>store atom’s data in a buffer (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>unpack_exchange</td>
|
||
|
|
<td>retrieve atom’s data from a buffer (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pack_restart</td>
|
||
|
|
<td>store atom’s data for writing to restart file (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>unpack_restart</td>
|
||
|
|
<td>retrieve atom’s data from a restart file buffer (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>size_restart</td>
|
||
|
|
<td>size of atom’s data (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>maxsize_restart</td>
|
||
|
|
<td>max size of atom’s data (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>setup_pre_force_respa</td>
|
||
|
|
<td>same as setup_pre_force, but for rRESPA (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>initial_integrate_respa</td>
|
||
|
|
<td>same as initial_integrate, but for rRESPA (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>post_integrate_respa</td>
|
||
|
|
<td>called after the first half integration step is done in rRESPA (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>pre_force_respa</td>
|
||
|
|
<td>same as pre_force, but for rRESPA (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>post_force_respa</td>
|
||
|
|
<td>same as post_force, but for rRESPA (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>final_integrate_respa</td>
|
||
|
|
<td>same as final_integrate, but for rRESPA (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>min_pre_force</td>
|
||
|
|
<td>called after pair & molecular forces are computed in minimizer (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>min_post_force</td>
|
||
|
|
<td>called after pair & molecular forces are computed and communicated in minmizer (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>min_store</td>
|
||
|
|
<td>store extra data for linesearch based minimization on a LIFO stack (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>min_pushstore</td>
|
||
|
|
<td>push the minimization LIFO stack one element down (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>min_popstore</td>
|
||
|
|
<td>pop the minimization LIFO stack one element up (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>min_clearstore</td>
|
||
|
|
<td>clear minimization LIFO stack (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>min_step</td>
|
||
|
|
<td>reset or move forward on line search minimization (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>min_dof</td>
|
||
|
|
<td>report number of degrees of freedom <em>added</em> by this fix in minimization (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>max_alpha</td>
|
||
|
|
<td>report maximum allowed step size during linesearch minimization (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>pack_comm</td>
|
||
|
|
<td>pack a buffer to communicate a per-atom quantity (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>unpack_comm</td>
|
||
|
|
<td>unpack a buffer to communicate a per-atom quantity (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>pack_reverse_comm</td>
|
||
|
|
<td>pack a buffer to reverse communicate a per-atom quantity (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>unpack_reverse_comm</td>
|
||
|
|
<td>unpack a buffer to reverse communicate a per-atom quantity (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>dof</td>
|
||
|
|
<td>report number of degrees of freedom <em>removed</em> by this fix during MD (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>compute_scalar</td>
|
||
|
|
<td>return a global scalar property that the fix computes (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>compute_vector</td>
|
||
|
|
<td>return a component of a vector property that the fix computes (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>compute_array</td>
|
||
|
|
<td>return a component of an array property that the fix computes (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>deform</td>
|
||
|
|
<td>called when the box size is changed (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>reset_target</td>
|
||
|
|
<td>called when a change of the target temperature is requested during a run (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>reset_dt</td>
|
||
|
|
<td>is called when a change of the time step is requested during a run (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>modify_param</td>
|
||
|
|
<td>called when a fix_modify request is executed (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>memory_usage</td>
|
||
|
|
<td>report memory used by fix (optional)</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>thermo</td>
|
||
|
|
<td>compute quantities for thermodynamic output (optional)</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
<p>Typically, only a small fraction of these methods are defined for a
|
||
|
|
particular fix. Setmask is mandatory, as it determines when the fix
|
||
|
|
will be invoked during the timestep. Fixes that perform time
|
||
|
|
integration (<em>nve</em>, <em>nvt</em>, <em>npt</em>) implement initial_integrate() and
|
||
|
|
final_integrate() to perform velocity Verlet updates. Fixes that
|
||
|
|
constrain forces implement post_force().</p>
|
||
|
|
<p>Fixes that perform diagnostics typically implement end_of_step(). For
|
||
|
|
an end_of_step fix, one of your fix arguments must be the variable
|
||
|
|
“nevery” which is used to determine when to call the fix and you must
|
||
|
|
set this variable in the constructor of your fix. By convention, this
|
||
|
|
is the first argument the fix defines (after the ID, group-ID, style).</p>
|
||
|
|
<p>If the fix needs to store information for each atom that persists from
|
||
|
|
timestep to timestep, it can manage that memory and migrate the info
|
||
|
|
with the atoms as they move from processors to processor by
|
||
|
|
implementing the grow_arrays, copy_arrays, pack_exchange, and
|
||
|
|
unpack_exchange methods. Similarly, the pack_restart and
|
||
|
|
unpack_restart methods can be implemented to store information about
|
||
|
|
the fix in restart files. If you wish an integrator or force
|
||
|
|
constraint fix to work with rRESPA (see the <a class="reference internal" href="run_style.html"><span class="doc">run_style</span></a>
|
||
|
|
command), the initial_integrate, post_force_integrate, and
|
||
|
|
final_integrate_respa methods can be implemented. The thermo method
|
||
|
|
enables a fix to contribute values to thermodynamic output, as printed
|
||
|
|
quantities and/or to be summed to the potential energy of the system.</p>
|
||
|
|
<hr class="docutils" />
|
||
|
|
</div>
|
||
|
|
<div class="section" id="input-script-commands">
|
||
|
|
<span id="mod-7"></span><h2>10.7. Input script commands</h2>
|
||
|
|
<p>New commands can be added to LAMMPS input scripts by adding new
|
||
|
|
classes that have a “command” method. For example, the create_atoms,
|
||
|
|
read_data, velocity, and run commands are all implemented in this
|
||
|
|
fashion. When such a command is encountered in the LAMMPS input
|
||
|
|
script, LAMMPS simply creates a class with the corresponding name,
|
||
|
|
invokes the “command” method of the class, and passes it the arguments
|
||
|
|
from the input script. The command method can perform whatever
|
||
|
|
operations it wishes on LAMMPS data structures.</p>
|
||
|
|
<p>The single method your new class must define is as follows:</p>
|
||
|
|
<table border="1" class="docutils">
|
||
|
|
<colgroup>
|
||
|
|
<col width="18%" />
|
||
|
|
<col width="82%" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody valign="top">
|
||
|
|
<tr class="row-odd"><td>command</td>
|
||
|
|
<td>operations performed by the new command</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
<p>Of course, the new class can define other methods and variables as
|
||
|
|
needed.</p>
|
||
|
|
<hr class="docutils" />
|
||
|
|
</div>
|
||
|
|
<div class="section" id="kspace-computations">
|
||
|
|
<span id="mod-8"></span><h2>10.8. Kspace computations</h2>
|
||
|
|
<p>Classes that compute long-range Coulombic interactions via K-space
|
||
|
|
representations (Ewald, PPPM) are derived from the KSpace class. New
|
||
|
|
styles can be created to add new K-space options to LAMMPS.</p>
|
||
|
|
<p>Ewald.cpp is an example of computing K-space interactions.</p>
|
||
|
|
<p>Here is a brief description of methods you define in your new derived
|
||
|
|
class. See kspace.h for details.</p>
|
||
|
|
<table border="1" class="docutils">
|
||
|
|
<colgroup>
|
||
|
|
<col width="23%" />
|
||
|
|
<col width="77%" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody valign="top">
|
||
|
|
<tr class="row-odd"><td>init</td>
|
||
|
|
<td>initialize the calculation before a run</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>setup</td>
|
||
|
|
<td>computation before the 1st timestep of a run</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>compute</td>
|
||
|
|
<td>every-timestep computation</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>memory_usage</td>
|
||
|
|
<td>tally of memory usage</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
<hr class="docutils" />
|
||
|
|
</div>
|
||
|
|
<div class="section" id="minimization-styles">
|
||
|
|
<span id="mod-9"></span><h2>10.9. Minimization styles</h2>
|
||
|
|
<p>Classes that perform energy minimization derived from the Min class.
|
||
|
|
New styles can be created to add new minimization algorithms to
|
||
|
|
LAMMPS.</p>
|
||
|
|
<p>Min_cg.cpp is an example of conjugate gradient minimization.</p>
|
||
|
|
<p>Here is a brief description of methods you define in your new derived
|
||
|
|
class. See min.h for details.</p>
|
||
|
|
<table border="1" class="docutils">
|
||
|
|
<colgroup>
|
||
|
|
<col width="25%" />
|
||
|
|
<col width="75%" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody valign="top">
|
||
|
|
<tr class="row-odd"><td>init</td>
|
||
|
|
<td>initialize the minimization before a run</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>run</td>
|
||
|
|
<td>perform the minimization</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>memory_usage</td>
|
||
|
|
<td>tally of memory usage</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
<hr class="docutils" />
|
||
|
|
</div>
|
||
|
|
<div class="section" id="pairwise-potentials">
|
||
|
|
<span id="mod-10"></span><h2>10.10. Pairwise potentials</h2>
|
||
|
|
<p>Classes that compute pairwise interactions are derived from the Pair
|
||
|
|
class. In LAMMPS, pairwise calculation include manybody potentials
|
||
|
|
such as EAM or Tersoff where particles interact without a static bond
|
||
|
|
topology. New styles can be created to add new pair potentials to
|
||
|
|
LAMMPS.</p>
|
||
|
|
<p>Pair_lj_cut.cpp is a simple example of a Pair class, though it
|
||
|
|
includes some optional methods to enable its use with rRESPA.</p>
|
||
|
|
<p>Here is a brief description of the class methods in pair.h:</p>
|
||
|
|
<table border="1" class="docutils">
|
||
|
|
<colgroup>
|
||
|
|
<col width="32%" />
|
||
|
|
<col width="68%" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody valign="top">
|
||
|
|
<tr class="row-odd"><td>compute</td>
|
||
|
|
<td>workhorse routine that computes pairwise interactions</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>settings</td>
|
||
|
|
<td>reads the input script line with arguments you define</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>coeff</td>
|
||
|
|
<td>set coefficients for one i,j type pair</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>init_one</td>
|
||
|
|
<td>perform initialization for one i,j type pair</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>init_style</td>
|
||
|
|
<td>initialization specific to this pair style</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>write & read_restart</td>
|
||
|
|
<td>write/read i,j pair coeffs to restart files</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>write & read_restart_settings</td>
|
||
|
|
<td>write/read global settings to restart files</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>single</td>
|
||
|
|
<td>force and energy of a single pairwise interaction between 2 atoms</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>compute_inner/middle/outer</td>
|
||
|
|
<td>versions of compute used by rRESPA</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
<p>The inner/middle/outer routines are optional.</p>
|
||
|
|
<hr class="docutils" />
|
||
|
|
</div>
|
||
|
|
<div class="section" id="region-styles">
|
||
|
|
<span id="mod-11"></span><h2>10.11. Region styles</h2>
|
||
|
|
<p>Classes that define geometric regions are derived from the Region
|
||
|
|
class. Regions are used elsewhere in LAMMPS to group atoms, delete
|
||
|
|
atoms to create a void, insert atoms in a specified region, etc. New
|
||
|
|
styles can be created to add new region shapes to LAMMPS.</p>
|
||
|
|
<p>Region_sphere.cpp is an example of a spherical region.</p>
|
||
|
|
<p>Here is a brief description of methods you define in your new derived
|
||
|
|
class. See region.h for details.</p>
|
||
|
|
<table border="1" class="docutils">
|
||
|
|
<colgroup>
|
||
|
|
<col width="21%" />
|
||
|
|
<col width="79%" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody valign="top">
|
||
|
|
<tr class="row-odd"><td>inside</td>
|
||
|
|
<td>determine whether a point is in the region</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>surface_interior</td>
|
||
|
|
<td>determine if a point is within a cutoff distance inside of surc</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>surface_exterior</td>
|
||
|
|
<td>determine if a point is within a cutoff distance outside of surf</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>shape_update</td>
|
||
|
|
<td>change region shape if set by time-depedent variable</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
<hr class="docutils" />
|
||
|
|
</div>
|
||
|
|
<div class="section" id="body-styles">
|
||
|
|
<span id="mod-12"></span><h2>10.12. Body styles</h2>
|
||
|
|
<p>Classes that define body particles are derived from the Body class.
|
||
|
|
Body particles can represent complex entities, such as surface meshes
|
||
|
|
of discrete points, collections of sub-particles, deformable objects,
|
||
|
|
etc.</p>
|
||
|
|
<p>See <a class="reference internal" href="Section_howto.html#howto-14"><span class="std std-ref">Section_howto 14</span></a> of the manual for
|
||
|
|
an overview of using body particles and the <a class="reference internal" href="body.html"><span class="doc">body</span></a> doc page
|
||
|
|
for details on the various body styles LAMMPS supports. New styles
|
||
|
|
can be created to add new kinds of body particles to LAMMPS.</p>
|
||
|
|
<p>Body_nparticle.cpp is an example of a body particle that is treated as
|
||
|
|
a rigid body containing N sub-particles.</p>
|
||
|
|
<p>Here is a brief description of methods you define in your new derived
|
||
|
|
class. See body.h for details.</p>
|
||
|
|
<table border="1" class="docutils">
|
||
|
|
<colgroup>
|
||
|
|
<col width="25%" />
|
||
|
|
<col width="75%" />
|
||
|
|
</colgroup>
|
||
|
|
<tbody valign="top">
|
||
|
|
<tr class="row-odd"><td>data_body</td>
|
||
|
|
<td>process a line from the Bodies section of a data file</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>noutrow</td>
|
||
|
|
<td>number of sub-particles output is generated for</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>noutcol</td>
|
||
|
|
<td>number of values per-sub-particle output is generated for</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>output</td>
|
||
|
|
<td>output values for the Mth sub-particle</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pack_comm_body</td>
|
||
|
|
<td>body attributes to communicate every timestep</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>unpack_comm_body</td>
|
||
|
|
<td>unpacking of those attributes</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-odd"><td>pack_border_body</td>
|
||
|
|
<td>body attributes to communicate when reneighboring is done</td>
|
||
|
|
</tr>
|
||
|
|
<tr class="row-even"><td>unpack_border_body</td>
|
||
|
|
<td>unpacking of those attributes</td>
|
||
|
|
</tr>
|
||
|
|
</tbody>
|
||
|
|
</table>
|
||
|
|
<hr class="docutils" />
|
||
|
|
</div>
|
||
|
|
<div class="section" id="thermodynamic-output-options">
|
||
|
|
<span id="mod-13"></span><h2>10.13. Thermodynamic output options</h2>
|
||
|
|
<p>There is one class that computes and prints thermodynamic information
|
||
|
|
to the screen and log file; see the file thermo.cpp.</p>
|
||
|
|
<p>There are two styles defined in thermo.cpp: “one” and “multi”. There
|
||
|
|
is also a flexible “custom” style which allows the user to explicitly
|
||
|
|
list keywords for quantities to print when thermodynamic info is
|
||
|
|
output. See the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command for a list
|
||
|
|
of defined quantities.</p>
|
||
|
|
<p>The thermo styles (one, multi, etc) are simply lists of keywords.
|
||
|
|
Adding a new style thus only requires defining a new list of keywords.
|
||
|
|
Search for the word “customize” with references to “thermo style” in
|
||
|
|
thermo.cpp to see the two locations where code will need to be added.</p>
|
||
|
|
<p>New keywords can also be added to thermo.cpp to compute new quantities
|
||
|
|
for output. Search for the word “customize” with references to
|
||
|
|
“keyword” in thermo.cpp to see the several locations where code will
|
||
|
|
need to be added.</p>
|
||
|
|
<p>Note that the <a class="reference internal" href="thermo.html"><span class="doc">thermo_style custom</span></a> command already allows
|
||
|
|
for thermo output of quantities calculated by <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 <a class="reference internal" href="variable.html"><span class="doc">variables</span></a>. Thus, it may
|
||
|
|
be simpler to compute what you wish via one of those constructs, than
|
||
|
|
by adding a new keyword to the thermo command.</p>
|
||
|
|
<hr class="docutils" />
|
||
|
|
</div>
|
||
|
|
<div class="section" id="variable-options">
|
||
|
|
<span id="mod-14"></span><h2>10.14. Variable options</h2>
|
||
|
|
<p>There is one class that computes and stores <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>
|
||
|
|
information in LAMMPS; see the file variable.cpp. The value
|
||
|
|
associated with a variable can be periodically printed to the screen
|
||
|
|
via the <a class="reference internal" href="print.html"><span class="doc">print</span></a>, <a class="reference internal" href="fix_print.html"><span class="doc">fix print</span></a>, or
|
||
|
|
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> commands. Variables of style
|
||
|
|
“equal” can compute complex equations that involve the following types
|
||
|
|
of arguments:</p>
|
||
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo</span> <span class="n">keywords</span> <span class="o">=</span> <span class="n">ke</span><span class="p">,</span> <span class="n">vol</span><span class="p">,</span> <span class="n">atoms</span><span class="p">,</span> <span class="o">...</span>
|
||
|
|
<span class="n">other</span> <span class="n">variables</span> <span class="o">=</span> <span class="n">v_a</span><span class="p">,</span> <span class="n">v_myvar</span><span class="p">,</span> <span class="o">...</span>
|
||
|
|
<span class="n">math</span> <span class="n">functions</span> <span class="o">=</span> <span class="n">div</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">),</span> <span class="n">mult</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">),</span> <span class="n">add</span><span class="p">(</span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">),</span> <span class="o">...</span>
|
||
|
|
<span class="n">group</span> <span class="n">functions</span> <span class="o">=</span> <span class="n">mass</span><span class="p">(</span><span class="n">group</span><span class="p">),</span> <span class="n">xcm</span><span class="p">(</span><span class="n">group</span><span class="p">,</span><span class="n">x</span><span class="p">),</span> <span class="o">...</span>
|
||
|
|
<span class="n">atom</span> <span class="n">values</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">123</span><span class="p">],</span> <span class="n">y</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">vx</span><span class="p">[</span><span class="mi">34</span><span class="p">],</span> <span class="o">...</span>
|
||
|
|
<span class="n">compute</span> <span class="n">values</span> <span class="o">=</span> <span class="n">c_mytemp</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="o">...</span>
|
||
|
|
</pre></div>
|
||
|
|
</div>
|
||
|
|
<p>Adding keywords for the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command
|
||
|
|
(which can then be accessed by variables) was discussed
|
||
|
|
<a class="reference internal" href="Section_howto.html#thermo"><span class="std std-ref">here</span></a> on this page.</p>
|
||
|
|
<p>Adding a new math function of one or two arguments can be done by
|
||
|
|
editing one section of the Variable::evaulate() method. Search for
|
||
|
|
the word “customize” to find the appropriate location.</p>
|
||
|
|
<p>Adding a new group function can be done by editing one section of the
|
||
|
|
Variable::evaulate() method. Search for the word “customize” to find
|
||
|
|
the appropriate location. You may need to add a new method to the
|
||
|
|
Group class as well (see the group.cpp file).</p>
|
||
|
|
<p>Accessing a new atom-based vector can be done by editing one section
|
||
|
|
of the Variable::evaulate() method. Search for the word “customize”
|
||
|
|
to find the appropriate location.</p>
|
||
|
|
<p>Adding new <a class="reference internal" href="compute.html"><span class="doc">compute styles</span></a> (whose calculated values can
|
||
|
|
then be accessed by variables) was discussed
|
||
|
|
<a class="reference internal" href="Section_howto.html#compute"><span class="std std-ref">here</span></a> on this page.</p>
|
||
|
|
</div>
|
||
|
|
<div class="section" id="submitting-new-features-for-inclusion-in-lammps">
|
||
|
|
<span id="mod-15"></span><h2>10.15. Submitting new features for inclusion in LAMMPS</h2>
|
||
|
|
<p>We encourage users to submit new features to <a class="reference external" href="http://lammps.sandia.gov/authors.html">the developers</a> that they add to
|
||
|
|
LAMMPS, especially if you think they will be of interest to other
|
||
|
|
users. The preferred way to do this is via GitHub. Once you have
|
||
|
|
prepared the content described below, see <a class="reference internal" href="tutorial_github.html"><span class="doc">this tutorial</span></a> for instructions on how to submit
|
||
|
|
your changes or new files.</p>
|
||
|
|
<p>If the new features/files are broadly useful we may add them as core
|
||
|
|
files to LAMMPS or as part of a <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">standard package</span></a>. Else we will add them as a
|
||
|
|
user-contributed file or package. Examples of user packages are in
|
||
|
|
src sub-directories that start with USER. The USER-MISC package is
|
||
|
|
simply a collection of (mostly) unrelated single files, which is the
|
||
|
|
simplest way to have your contribution quickly added to the LAMMPS
|
||
|
|
distribution. You can see a list of the both standard and user
|
||
|
|
packages by typing “make package” in the LAMMPS src directory.</p>
|
||
|
|
<p>Note that by providing us files to release, you are agreeing to make
|
||
|
|
them open-source, i.e. we can release them under the terms of the GPL,
|
||
|
|
used as a license for the rest of LAMMPS. See <a class="reference internal" href="Section_intro.html#intro-4"><span class="std std-ref">Section 1.4</span></a> for details.</p>
|
||
|
|
<p>With user packages and files, all we are really providing (aside from
|
||
|
|
the fame and fortune that accompanies having your name in the source
|
||
|
|
code and on the <a class="reference external" href="http://lammps.sandia.gov/authors.html">Authors page</a>
|
||
|
|
of the <a class="reference external" href="http://lammps.sandia.gov">LAMMPS WWW site</a>), is a means for you to distribute your
|
||
|
|
work to the LAMMPS user community, and a mechanism for others to
|
||
|
|
easily try out your new feature. This may help you find bugs or make
|
||
|
|
contact with new collaborators. Note that you’re also implicitly
|
||
|
|
agreeing to support your code which means answer questions, fix bugs,
|
||
|
|
and maintain it if LAMMPS changes in some way that breaks it (an
|
||
|
|
unusual event).</p>
|
||
|
|
<div class="admonition note">
|
||
|
|
<p class="first admonition-title">Note</p>
|
||
|
|
<p class="last">If you prefer to actively develop and support your add-on
|
||
|
|
feature yourself, then you may wish to make it available for download
|
||
|
|
from your own website, as a user package that LAMMPS users can add to
|
||
|
|
their copy of LAMMPS. See the <a class="reference external" href="http://lammps.sandia.gov/offsite.html">Offsite LAMMPS packages and tools</a> page of the LAMMPS web
|
||
|
|
site for examples of groups that do this. We are happy to advertise
|
||
|
|
your package and web site from that page. Simply email the
|
||
|
|
<a class="reference external" href="http://lammps.sandia.gov/authors.html">developers</a> with info about
|
||
|
|
your package and we will post it there.</p>
|
||
|
|
</div>
|
||
|
|
<p>The previous sections of this doc page describe how to add new “style”
|
||
|
|
files of various kinds to LAMMPS. Packages are simply collections of
|
||
|
|
one or more new class files which are invoked as a new style within a
|
||
|
|
LAMMPS input script. If designed correctly, these additions typically
|
||
|
|
do not require changes to the main core of LAMMPS; they are simply
|
||
|
|
add-on files. If you think your new feature requires non-trivial
|
||
|
|
changes in core LAMMPS files, you’ll need to <a class="reference external" href="http://lammps.sandia.gov/authors.html">communicate with the developers</a>, since we may or may
|
||
|
|
not want to make those changes. An example of a trivial change is
|
||
|
|
making a parent-class method “virtual” when you derive a new child
|
||
|
|
class from it.</p>
|
||
|
|
<p>Here are the steps you need to follow to submit a single file or user
|
||
|
|
package for our consideration. Following these steps will save both
|
||
|
|
you and us time. See existing files in packages in the src dir for
|
||
|
|
examples.</p>
|
||
|
|
<ul class="simple">
|
||
|
|
<li>All source files you provide must compile with the most current
|
||
|
|
version of LAMMPS.</li>
|
||
|
|
<li>If you want your file(s) to be added to main LAMMPS or one of its
|
||
|
|
standard packages, then it needs to be written in a style compatible
|
||
|
|
with other LAMMPS source files. This is so the developers can
|
||
|
|
understand it and hopefully maintain it. This basically means that
|
||
|
|
the code accesses data structures, performs its operations, and is
|
||
|
|
formatted similar to other LAMMPS source files, including the use of
|
||
|
|
the error class for error and warning messages.</li>
|
||
|
|
<li>If you want your contribution to be added as a user-contributed
|
||
|
|
feature, and it’s a single file (actually a <a href="#id8"><span class="problematic" id="id9">*</span></a>.cpp and <a href="#id10"><span class="problematic" id="id11">*</span></a>.h file) it can
|
||
|
|
rapidly be added to the USER-MISC directory. Send us the one-line
|
||
|
|
entry to add to the USER-MISC/README file in that dir, along with the
|
||
|
|
2 source files. You can do this multiple times if you wish to
|
||
|
|
contribute several individual features.</li>
|
||
|
|
<li>If you want your contribution to be added as a user-contribution and
|
||
|
|
it is several related featues, it is probably best to make it a user
|
||
|
|
package directory with a name like USER-FOO. In addition to your new
|
||
|
|
files, the directory should contain a README text file. The README
|
||
|
|
should contain your name and contact information and a brief
|
||
|
|
description of what your new package does. If your files depend on
|
||
|
|
other LAMMPS style files also being installed (e.g. because your file
|
||
|
|
is a derived class from the other LAMMPS class), then an Install.sh
|
||
|
|
file is also needed to check for those dependencies. See other README
|
||
|
|
and Install.sh files in other USER directories as examples. Send us a
|
||
|
|
tarball of this USER-FOO directory.</li>
|
||
|
|
<li>Your new source files need to have the LAMMPS copyright, GPL notice,
|
||
|
|
and your name and email address at the top, like other
|
||
|
|
user-contributed LAMMPS source files. They need to create a class
|
||
|
|
that is inside the LAMMPS namespace. If the file is for one of the
|
||
|
|
USER packages, including USER-MISC, then we are not as picky about the
|
||
|
|
coding style (see above). I.e. the files do not need to be in the
|
||
|
|
same stylistic format and syntax as other LAMMPS files, though that
|
||
|
|
would be nice for developers as well as users who try to read your
|
||
|
|
code.</li>
|
||
|
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<li>You must also create a documentation file for each new command or
|
||
|
|
style you are adding to LAMMPS. This will be one file for a
|
||
|
|
single-file feature. For a package, it might be several files. These
|
||
|
|
are simple text files which we auto-convert to HTML. Thus they must
|
||
|
|
be in the same format as other <em>.txt files in the lammps/doc directory
|
||
|
|
for similar commands and styles; use one or more of them as a starting
|
||
|
|
point. As appropriate, the text files can include links to equations
|
||
|
|
(see doc/Eqs/</em>.tex for examples, we auto-create the associated JPG
|
||
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files), or figures (see doc/JPG for examples), or even additional PDF
|
||
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files with further details (see doc/PDF for examples). The doc page
|
||
|
|
should also include literature citations as appropriate; see the
|
||
|
|
bottom of doc/fix_nh.txt for examples and the earlier part of the same
|
||
|
|
file for how to format the cite itself. The “Restrictions” section of
|
||
|
|
the doc page should indicate that your command is only available if
|
||
|
|
LAMMPS is built with the appropriate USER-MISC or USER-FOO package.
|
||
|
|
See other user package doc files for examples of how to do this. The
|
||
|
|
txt2html tool we use to convert to HTML can be downloaded from <a class="reference external" href="http://www.sandia.gov/~sjplimp/download.html">this site</a>, so you can perform
|
||
|
|
the HTML conversion yourself to proofread your doc page.</li>
|
||
|
|
<li>For a new package (or even a single command) you can include one or
|
||
|
|
more example scripts. These should run in no more than 1 minute, even
|
||
|
|
on a single processor, and not require large data files as input. See
|
||
|
|
directories under examples/USER for examples of input scripts other
|
||
|
|
users provided for their packages.</li>
|
||
|
|
<li>If there is a paper of yours describing your feature (either the
|
||
|
|
algorithm/science behind the feature itself, or its initial usage, or
|
||
|
|
its implementation in LAMMPS), you can add the citation to the <a href="#id12"><span class="problematic" id="id13">*</span></a>.cpp
|
||
|
|
source file. See src/USER-EFF/atom_vec_electron.cpp for an example.
|
||
|
|
A LaTeX citation is stored in a variable at the top of the file and a
|
||
|
|
single line of code that references the variable is added to the
|
||
|
|
constructor of the class. Whenever a user invokes your feature from
|
||
|
|
their input script, this will cause LAMMPS to output the citation to a
|
||
|
|
log.cite file and prompt the user to examine the file. Note that you
|
||
|
|
should only use this for a paper you or your group authored.
|
||
|
|
E.g. adding a cite in the code for a paper by Nose and Hoover if you
|
||
|
|
write a fix that implements their integrator is not the intended
|
||
|
|
usage. That kind of citation should just be in the doc page you
|
||
|
|
provide.</li>
|
||
|
|
</ul>
|
||
|
|
<p>Finally, as a general rule-of-thumb, the more clear and
|
||
|
|
self-explanatory you make your doc and README files, and the easier
|
||
|
|
you make it for people to get started, e.g. by providing example
|
||
|
|
scripts, the more likely it is that users will try out your new
|
||
|
|
feature.</p>
|
||
|
|
<p id="foo"><strong>(Foo)</strong> Foo, Morefoo, and Maxfoo, J of Classic Potentials, 75, 345 (1997).</p>
|
||
|
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