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<title>Body particles — LAMMPS documentation</title>
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<a href="Manual.html" class="icon icon-home"> LAMMPS
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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 role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
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<div class="section" id="body-particles">
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<h1>Body particles</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 class="std std-ref">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"><span class="doc">atom_style body</span></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"><span class="doc">atom_style body</span></a> command.</p>
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<table border="1" class="docutils">
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<colgroup>
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<col width="35%" />
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<col width="65%" />
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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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<tr class="row-even"><td><em>rounded/polygon</em></td>
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<td>2d convex polygon with N vertices</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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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">The rounded/polygon style listed in the table above and
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described below has not yet been relesed in LAMMPS. It will be soon.</p>
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</div>
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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 class="std std-ref">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"><span class="doc">fix rigid</span></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"><span class="doc">fix rigid</span></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"><span class="doc">fix rigid</span></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"><span class="doc">fix rigid</span></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"><span class="doc">fix nve/body</span></a></td>
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<td>integrate motion of a body particle in NVE ensemble</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="fix_nvt_body.html"><span class="doc">fix nvt/body</span></a></td>
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<td>ditto for NVT ensemble</td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="fix_npt_body.html"><span class="doc">fix npt/body</span></a></td>
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<td>ditto for NPT ensemble</td>
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</tr>
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<tr class="row-even"><td><a class="reference internal" href="fix_nph_body.html"><span class="doc">fix nph/body</span></a></td>
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<td>ditto for NPH ensemble</td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="compute_body_local.html"><span class="doc">compute body/local</span></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-even"><td><a class="reference internal" href="compute_temp_body.html"><span class="doc">compute temp/body</span></a></td>
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<td>compute temperature of body particles</td>
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</tr>
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<tr class="row-odd"><td><a class="reference internal" href="dump.html"><span class="doc">dump local</span></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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<tr class="row-even"><td><a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a></td>
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<td>output body particle attributes as an image</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"><span class="doc">fix rigid</span></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-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
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<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of sub-particles in any body in the system</span>
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<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of sub-particles in any body in the system</span>
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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"><span class="doc">read_data</span></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-default"><div class="highlight"><pre><span></span><span class="n">atom</span><span class="o">-</span><span class="n">ID</span> <span class="mi">1</span> <span class="n">M</span>
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<span class="n">N</span>
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<span class="n">ixx</span> <span class="n">iyy</span> <span class="n">izz</span> <span class="n">ixy</span> <span class="n">ixz</span> <span class="n">iyz</span>
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<span class="n">x1</span> <span class="n">y1</span> <span class="n">z1</span>
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<span class="o">...</span>
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<span class="n">xN</span> <span class="n">yN</span> <span class="n">zN</span>
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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. These values can be listed on
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as many lines as you wish; see the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command
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for more details.</p>
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<p>The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
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values consistent with the current orientation of the rigid body
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around its center of mass. The values are with respect to the
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simulation box XYZ axes, not with respect to the prinicpal axes of the
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rigid body itself. LAMMPS performs the latter calculation internally.
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The coordinates of each sub-particle are specified as its x,y,z
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displacement from the center-of-mass of the body particle. The
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center-of-mass position of the particle is specified by the x,y,z
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values in the <em>Atoms</em> section of the data file, as is the total mass
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of the body particle.</p>
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<p>The <a class="reference internal" href="pair_body.html"><span class="doc">pair_style body</span></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"><span class="doc">compute body/local</span></a> and <a class="reference internal" href="dump.html"><span class="doc">dump local</span></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-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="o">=</span> <span class="n">x</span> <span class="n">position</span> <span class="n">of</span> <span class="n">sub</span><span class="o">-</span><span class="n">particle</span>
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<span class="mi">2</span> <span class="o">=</span> <span class="n">y</span> <span class="n">position</span> <span class="n">of</span> <span class="n">sub</span><span class="o">-</span><span class="n">particle</span>
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<span class="mi">3</span> <span class="o">=</span> <span class="n">z</span> <span class="n">position</span> <span class="n">of</span> <span class="n">sub</span><span class="o">-</span><span class="n">particle</span>
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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 orientation of the body particle.</p>
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<p>For images created by the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> command, if the
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<em>body</em> keyword is set, then each body particle is drawn as a
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collection of spheres, one for each sub-particle. The size of each
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sphere is determined by the <em>bflag1</em> parameter for the <em>body</em> keyword.
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The <em>bflag2</em> argument is ignored.</p>
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<hr class="docutils" />
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<p><strong>Specifics of body style rounded/polygon:</strong></p>
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<p>The <em>rounded/polygon</em> body style represents body particles as a convex
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polygon with a variable number N > 2 of vertices, which can only be
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used for 2d models. One example use of this body style is for 2d
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discrete element models, as described in <a class="reference internal" href="#fraige"><span class="std std-ref">Fraige</span></a>. Similar to
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body style <em>nparticle</em>, the atom_style body command for this body
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style takes two additional arguments:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">rounded</span><span class="o">/</span><span class="n">polygon</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
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<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of vertices in any body in the system</span>
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<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of vertices in any body in the system</span>
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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"><span class="doc">read_data</span></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-default"><div class="highlight"><pre><span></span><span class="n">atom</span><span class="o">-</span><span class="n">ID</span> <span class="mi">1</span> <span class="n">M</span>
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<span class="n">N</span>
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<span class="n">ixx</span> <span class="n">iyy</span> <span class="n">izz</span> <span class="n">ixy</span> <span class="n">ixz</span> <span class="n">iyz</span>
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<span class="n">x1</span> <span class="n">y1</span> <span class="n">z1</span>
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<span class="o">...</span>
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<span class="n">xN</span> <span class="n">yN</span> <span class="n">zN</span>
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<span class="n">i</span> <span class="n">j</span> <span class="n">j</span> <span class="n">k</span> <span class="n">k</span> <span class="o">...</span>
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<span class="n">radius</span>
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</pre></div>
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</div>
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<p>N is the number of vertices in the body particle. M = 6 + 3*N + 2*N +
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1. 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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vertices (x1 to zN) as 3N values, followed by 2N vertex indices
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corresponding to the end points of the N edges, followed by a single
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radius value = the smallest circle encompassing the polygon. That
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last value is used to facilitate the body/body contact detection.
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These floating-point values can be listed on as many lines as you
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wish; see the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command for more details.</p>
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<p>The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz) should be the
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values consistent with the current orientation of the rigid body
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around its center of mass. The values are with respect to the
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simulation box XYZ axes, not with respect to the prinicpal axes of the
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rigid body itself. LAMMPS performs the latter calculation internally.
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The coordinates of each vertex are specified as its x,y,z displacement
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from the center-of-mass of the body particle. The center-of-mass
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position of the particle is specified by the x,y,z values in the
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<em>Atoms</em> section of the data file.</p>
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<p>For example, the following information would specify a square
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particles whose edge length is sqrt(2):</p>
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|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">3</span> <span class="mi">1</span> <span class="mi">27</span>
|
|
<span class="mi">4</span>
|
|
<span class="mi">1</span> <span class="mi">1</span> <span class="mi">4</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span>
|
|
<span class="o">-</span><span class="mf">0.7071</span> <span class="o">-</span><span class="mf">0.7071</span> <span class="mi">0</span>
|
|
<span class="o">-</span><span class="mf">0.7071</span> <span class="mf">0.7071</span> <span class="mi">0</span>
|
|
<span class="mf">0.7071</span> <span class="mf">0.7071</span> <span class="mi">0</span>
|
|
<span class="mf">0.7071</span> <span class="o">-</span><span class="mf">0.7071</span> <span class="mi">0</span>
|
|
<span class="mi">0</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mi">3</span> <span class="mi">0</span>
|
|
<span class="mf">1.0</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>The <span class="xref doc">pair_style body/rounded/polygon</span> command
|
|
can be used with this body style to compute body/body interactions.</p>
|
|
<p>For output purposes via the <a class="reference internal" href="compute_body_local.html"><span class="doc">compute body/local</span></a> and <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>
|
|
commands, this body style produces one datum for each of the N
|
|
sub-particles in a body particle. The datum has 3 values:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="o">=</span> <span class="n">x</span> <span class="n">position</span> <span class="n">of</span> <span class="n">vertex</span>
|
|
<span class="mi">2</span> <span class="o">=</span> <span class="n">y</span> <span class="n">position</span> <span class="n">of</span> <span class="n">vertex</span>
|
|
<span class="mi">3</span> <span class="o">=</span> <span class="n">z</span> <span class="n">position</span> <span class="n">of</span> <span class="n">vertex</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>These values are the current position of the vertex within the
|
|
simulation domain, not a displacement from the center-of-mass (COM) of
|
|
the body particle itself. These values are calculated using the
|
|
current COM and orientation of the body particle.</p>
|
|
<p>For images created by the <a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> command, if the
|
|
<em>body</em> keyword is set, then each body particle is drawn as a convex
|
|
polygon consisting of N line segments. Note that the line segments
|
|
are drawn between the N vertices, which does not correspond exactly to
|
|
the physical extent of the body (because the <a class="reference external" href="pair_body_rounded_polygon.cpp">pair_style rounded/polygon</a> defines finite-size
|
|
spheres at those point and the line segments between the spheres are
|
|
tangent to the spheres). The drawn diameter of each line segment is
|
|
determined by the <em>bflag1</em> parameter for the <em>body</em> keyword. The
|
|
<em>bflag2</em> argument is ignored.</p>
|
|
<hr class="docutils" />
|
|
<p id="fraige"><strong>(Fraige)</strong> F. Y. Fraige, P. A. Langston, A. J. Matchett, J. Dodds,
|
|
Particuology, 6, 455 (2008).</p>
|
|
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