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<title>Body particles — LAMMPS 15 May 2015 version documentation</title>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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<li>Body particles</li>
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<div class="section" id="body-particles">
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<h1>Body particles<a class="headerlink" href="#body-particles" title="Permalink to this headline">¶</a></h1>
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<p><strong>Overview:</strong></p>
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<p>This doc page is not about a LAMMPS input script command, but about
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body particles, which are generalized finite-size particles.
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Individual body particles can represent complex entities, such as
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surface meshes of discrete points, collections of sub-particles,
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deformable objects, etc. Note that other kinds of finite-size
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spherical and aspherical particles are also supported by LAMMPS, such
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as spheres, ellipsoids, line segments, and triangles, but they are
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simpler entities that body particles. See <a class="reference internal" href="Section_howto.html#howto-14"><span>Section_howto 14</span></a> for a general overview of all these
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particle types.</p>
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<p>Body particles are used via the <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a>
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command. It takes a body style as an argument. The current body
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styles supported by LAMMPS are as follows. The name in the first
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column is used as the <em>bstyle</em> argument for the <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a> command.</p>
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<table border="1" class="docutils">
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<colgroup>
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<col width="28%" />
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<col width="72%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td><em>nparticle</em></td>
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<td>rigid body with N sub-particles</td>
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</tr>
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</tbody>
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</table>
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<p>The body style determines what attributes are stored for each body and
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thus how they can be used to compute pairwise body/body or
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bond/non-body (point particle) interactions. More details of each
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style are described below.</p>
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<p>We hope to add more styles in the future. See <a class="reference internal" href="Section_modify.html#mod-12"><span>Section_modify 12</span></a> for details on how to add a new body
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style to the code.</p>
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<hr class="docutils" />
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<p><strong>When to use body particles:</strong></p>
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<p>You should not use body particles to model a rigid body made of
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simpler particles (e.g. point, sphere, ellipsoid, line segment,
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triangular particles), if the interaction between pairs of rigid
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bodies is just the summation of pairwise interactions between the
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simpler particles. LAMMPS already supports this kind of model via the
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<a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command. Any of the numerous pair styles
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that compute interactions between simpler particles can be used. The
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<a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command time integrates the motion of the
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rigid bodies. All of the standard LAMMPS commands for thermostatting,
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adding constraints, performing output, etc will operate as expected on
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the simple particles.</p>
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<p>By contrast, when body particles are used, LAMMPS treats an entire
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body as a single particle for purposes of computing pairwise
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interactions, building neighbor lists, migrating particles between
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processors, outputting particles to a dump file, etc. This means that
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interactions between pairs of bodies or between a body and non-body
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(point) particle need to be encoded in an appropriate pair style. If
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such a pair style were to mimic the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> model,
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it would need to loop over the entire collection of interactions
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between pairs of simple particles within the two bodies, each time a
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single body/body interaction was computed.</p>
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<p>Thus it only makes sense to use body particles and develop such a pair
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style, when particle/particle interactions are more complex than what
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the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command can already calculate. For
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example, if particles have one or more of the following attributes:</p>
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<ul class="simple">
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<li>represented by a surface mesh</li>
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<li>represented by a collection of geometric entities (e.g. planes + spheres)</li>
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<li>deformable</li>
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<li>internal stress that induces fragmentation</li>
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</ul>
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<p>then the interaction between pairs of particles is likely to be more
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complex than the summation of simple sub-particle interactions. An
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example is contact or frictional forces between particles with planar
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sufaces that inter-penetrate.</p>
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<p>These are additional LAMMPS commands that can be used with body
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particles of different styles</p>
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<table border="1" class="docutils">
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<colgroup>
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<col width="48%" />
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<col width="52%" />
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</colgroup>
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<tbody valign="top">
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<tr class="row-odd"><td><a class="reference internal" href="fix_nve_body.html"><em>fix nve/body</em></a></td>
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<td>integrate motion of a body particle</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="compute_body_local.html"><em>compute body/local</em></a></td>
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<td>store sub-particle attributes of a body particle</td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="dump.html"><em>dump local</em></a></td>
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<td>output sub-particle attributes of a body particle</td>
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</tr>
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</tbody>
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</table>
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<p>The pair styles defined for use with specific body styles are listed
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in the sections below.</p>
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<hr class="docutils" />
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<p><strong>Specifics of body style nparticle:</strong></p>
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<p>The <em>nparticle</em> body style represents body particles as a rigid body
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with a variable number N of sub-particles. It is provided as a
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vanillia, prototypical example of a body particle, although as
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mentioned above, the <a class="reference internal" href="fix_rigid.html"><em>fix rigid</em></a> command already
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duplicates its functionality.</p>
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<p>The atom_style body command for this body style takes two additional
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arguments:</p>
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<div class="highlight-python"><div class="highlight"><pre>atom_style body nparticle Nmin Nmax
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Nmin = minimum # of sub-particles in any body in the system
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Nmax = maximum # of sub-particles in any body in the system
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</pre></div>
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</div>
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<p>The Nmin and Nmax arguments are used to bound the size of data
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structures used internally by each particle.</p>
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<p>When the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command reads a data file for this
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body style, the following information must be provided for each entry
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in the <em>Bodies</em> section of the data file:</p>
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<div class="highlight-python"><div class="highlight"><pre>atom-ID 1 M
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N
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ixx iyy izz ixy ixz iyz x1 y1 z1 ...
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...
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... xN yN zN
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</pre></div>
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</div>
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<p>N is the number of sub-particles in the body particle. M = 6 + 3*N.
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The integer line has a single value N. The floating point line(s)
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list 6 moments of inertia followed by the coordinates of the N
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sub-particles (x1 to zN) as 3N values on as many lines as required.
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Note that this in not N lines, but 10 values per line; see the
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<a class="reference internal" href="read_data.html"><em>read_data</em></a> command for details. The 6 moments of
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inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the values consistent with
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the current orientation of the rigid body around its center of mass.
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The values are with respect to the simulation box XYZ axes, not with
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respect to the prinicpal axes of the rigid body itself. LAMMPS
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performs the latter calculation internally. The coordinates of each
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sub-particle are specified as its x,y,z displacement from the
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center-of-mass of the body particle. The center-of-mass position of
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the particle is specified by the x,y,z values in the <em>Atoms</em> section
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of the data file.</p>
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<p>The <a class="reference internal" href="pair_body.html"><em>pair_style body</em></a> command can be used with this
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body style to compute body/body and body/non-body interactions.</p>
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<p>For output purposes via the <a class="reference internal" href="compute_body_local.html"><em>compute body/local</em></a> and <a class="reference internal" href="dump.html"><em>dump local</em></a>
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commands, this body style produces one datum for each of the N
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sub-particles in a body particle. The datum has 3 values:</p>
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<div class="highlight-python"><div class="highlight"><pre>1 = x position of sub-particle
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2 = y position of sub-particle
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3 = z position of sub-particle
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</pre></div>
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</div>
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<p>These values are the current position of the sub-particle within the
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simulation domain, not a displacement from the center-of-mass (COM) of
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the body particle itself. These values are calculated using the
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current COM and orientiation of the body particle.</p>
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