262 lines
14 KiB
HTML
262 lines
14 KiB
HTML
<!DOCTYPE html>
|
|
<html class="writer-html5" lang="en" >
|
|
<head>
|
|
<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
|
|
|
|
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
|
|
<title>8.5.10. Manifolds (surfaces) — LAMMPS documentation</title>
|
|
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
|
|
<link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
|
|
<link rel="stylesheet" href="_static/sphinx-design.min.css" type="text/css" />
|
|
<link rel="stylesheet" href="_static/css/lammps.css" type="text/css" />
|
|
<link rel="shortcut icon" href="_static/lammps.ico"/>
|
|
<link rel="canonical" href="https://docs.lammps.org/Howto_manifold.html" />
|
|
<!--[if lt IE 9]>
|
|
<script src="_static/js/html5shiv.min.js"></script>
|
|
<![endif]-->
|
|
|
|
<script src="_static/jquery.js?v=5d32c60e"></script>
|
|
<script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
|
|
<script src="_static/documentation_options.js?v=5929fcd5"></script>
|
|
<script src="_static/doctools.js?v=9bcbadda"></script>
|
|
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
|
|
<script src="_static/design-tabs.js?v=f930bc37"></script>
|
|
<script async="async" src="_static/mathjax/es5/tex-mml-chtml.js?v=cadf963e"></script>
|
|
<script src="_static/js/theme.js"></script>
|
|
<link rel="index" title="Index" href="genindex.html" />
|
|
<link rel="search" title="Search" href="search.html" />
|
|
<link rel="next" title="8.5.11. Reproducing hydrodynamics and elastic objects (RHEO)" href="Howto_rheo.html" />
|
|
<link rel="prev" title="8.5.9. Peridynamics with LAMMPS" href="Howto_peri.html" />
|
|
</head>
|
|
|
|
<body class="wy-body-for-nav">
|
|
<div class="wy-grid-for-nav">
|
|
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
|
|
<div class="wy-side-scroll">
|
|
<div class="wy-side-nav-search" >
|
|
|
|
|
|
|
|
<a href="Manual.html">
|
|
|
|
<img src="_static/lammps-logo.png" class="logo" alt="Logo"/>
|
|
</a>
|
|
<div class="lammps_version">Version: <b>19 Nov 2024</b></div>
|
|
<div class="lammps_release">git info: </div>
|
|
<div role="search">
|
|
<form id="rtd-search-form" class="wy-form" action="search.html" method="get">
|
|
<input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
|
|
<input type="hidden" name="check_keywords" value="yes" />
|
|
<input type="hidden" name="area" value="default" />
|
|
</form>
|
|
</div>
|
|
</div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
|
|
<p class="caption" role="heading"><span class="caption-text">User Guide</span></p>
|
|
<ul class="current">
|
|
<li class="toctree-l1"><a class="reference internal" href="Intro.html">1. Introduction</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Install.html">2. Install LAMMPS</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Build.html">3. Build LAMMPS</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Run_head.html">4. Run LAMMPS</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Commands.html">5. Commands</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Packages.html">6. Optional packages</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Speed.html">7. Accelerate performance</a></li>
|
|
<li class="toctree-l1 current"><a class="reference internal" href="Howto.html">8. Howto discussions</a><ul class="current">
|
|
<li class="toctree-l2"><a class="reference internal" href="Howto.html#general-howto">8.1. General howto</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="Howto.html#settings-howto">8.2. Settings howto</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="Howto.html#analysis-howto">8.3. Analysis howto</a></li>
|
|
<li class="toctree-l2"><a class="reference internal" href="Howto.html#force-fields-howto">8.4. Force fields howto</a></li>
|
|
<li class="toctree-l2 current"><a class="reference internal" href="Howto.html#packages-howto">8.5. Packages howto</a><ul class="current">
|
|
<li class="toctree-l3"><a class="reference internal" href="Howto_spherical.html">8.5.1. Finite-size spherical and aspherical particles</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="Howto_granular.html">8.5.2. Granular models</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="Howto_body.html">8.5.3. Body particles</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="Howto_bpm.html">8.5.4. Bonded particle models</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="Howto_polarizable.html">8.5.5. Polarizable models</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="Howto_coreshell.html">8.5.6. Adiabatic core/shell model</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="Howto_drude.html">8.5.7. Drude induced dipoles</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="Howto_drude2.html">8.5.8. Tutorial for Thermalized Drude oscillators in LAMMPS</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="Howto_peri.html">8.5.9. Peridynamics with LAMMPS</a></li>
|
|
<li class="toctree-l3 current"><a class="current reference internal" href="#">8.5.10. Manifolds (surfaces)</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="Howto_rheo.html">8.5.11. Reproducing hydrodynamics and elastic objects (RHEO)</a></li>
|
|
<li class="toctree-l3"><a class="reference internal" href="Howto_spins.html">8.5.12. Magnetic spins</a></li>
|
|
</ul>
|
|
</li>
|
|
<li class="toctree-l2"><a class="reference internal" href="Howto.html#tutorials-howto">8.6. Tutorials howto</a></li>
|
|
</ul>
|
|
</li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Examples.html">9. Example scripts</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Tools.html">10. Auxiliary tools</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Errors.html">11. Errors</a></li>
|
|
</ul>
|
|
<p class="caption" role="heading"><span class="caption-text">Programmer Guide</span></p>
|
|
<ul>
|
|
<li class="toctree-l1"><a class="reference internal" href="Library.html">1. LAMMPS Library Interfaces</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Python_head.html">2. Use Python with LAMMPS</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Modify.html">3. Modifying & extending LAMMPS</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Developer.html">4. Information for Developers</a></li>
|
|
</ul>
|
|
<p class="caption" role="heading"><span class="caption-text">Command Reference</span></p>
|
|
<ul>
|
|
<li class="toctree-l1"><a class="reference internal" href="commands_list.html">Commands</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="computes.html">Compute Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="impropers.html">Improper Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="dumps.html">Dump Styles</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="fix_modify_atc_commands.html">fix_modify AtC commands</a></li>
|
|
<li class="toctree-l1"><a class="reference internal" href="Bibliography.html">Bibliography</a></li>
|
|
</ul>
|
|
|
|
</div>
|
|
</div>
|
|
</nav>
|
|
|
|
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
|
|
<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
|
|
<a href="Manual.html">LAMMPS</a>
|
|
</nav>
|
|
|
|
<div class="wy-nav-content">
|
|
<div class="rst-content style-external-links">
|
|
<div role="navigation" aria-label="Page navigation">
|
|
<ul class="wy-breadcrumbs">
|
|
<li><a href="Manual.html" class="icon icon-home" aria-label="Home"></a></li>
|
|
<li class="breadcrumb-item"><a href="Howto.html"><span class="section-number">8. </span>Howto discussions</a></li>
|
|
<li class="breadcrumb-item active"><span class="section-number">8.5.10. </span>Manifolds (surfaces)</li>
|
|
<li class="wy-breadcrumbs-aside">
|
|
<a href="https://www.lammps.org"><img src="_static/lammps-logo.png" width="64" height="16" alt="LAMMPS Homepage"></a> | <a href="Commands_all.html">Commands</a>
|
|
</li>
|
|
</ul><div class="rst-breadcrumbs-buttons" role="navigation" aria-label="Sequential page navigation">
|
|
<a href="Howto_peri.html" class="btn btn-neutral float-left" title="8.5.9. Peridynamics with LAMMPS" accesskey="p"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
|
|
<a href="Howto_rheo.html" class="btn btn-neutral float-right" title="8.5.11. Reproducing hydrodynamics and elastic objects (RHEO)" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
|
|
</div>
|
|
<hr/>
|
|
</div>
|
|
<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
|
<div itemprop="articleBody">
|
|
|
|
<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
|
|
<section id="manifolds-surfaces">
|
|
<h1><span class="section-number">8.5.10. </span>Manifolds (surfaces)<a class="headerlink" href="#manifolds-surfaces" title="Link to this heading"></a></h1>
|
|
<p><strong>Overview:</strong></p>
|
|
<p>This page is not about a LAMMPS input script command, but about
|
|
manifolds, which are generalized surfaces, as defined and used by the
|
|
MANIFOLD package, to track particle motion on the manifolds. See
|
|
the src/MANIFOLD/README file for more details about the package
|
|
and its commands.</p>
|
|
<p>Below is a list of currently supported manifolds by the MANIFOLD
|
|
package, their parameters and a short description of them. The
|
|
parameters listed here are in the same order as they should be passed
|
|
to the relevant fixes.</p>
|
|
<table class="docutils align-default">
|
|
<tbody>
|
|
<tr class="row-odd"><td><p><em>manifold</em></p></td>
|
|
<td><p><em>parameters</em></p></td>
|
|
<td><p><em>equation</em></p></td>
|
|
<td><p><em>description</em></p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>cylinder</p></td>
|
|
<td><p>R</p></td>
|
|
<td><p>x^2 + y^2 - R^2 = 0</p></td>
|
|
<td><p>Cylinder along z-axis, axis going through (0,0,0)</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>cylinder_dent</p></td>
|
|
<td><p>R l a</p></td>
|
|
<td><p>x^2 + y^2 - r(z)^2 = 0, r(x) = R if | z | > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise</p></td>
|
|
<td><p>A cylinder with a dent around z = 0</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>dumbbell</p></td>
|
|
<td><p>a A B c</p></td>
|
|
<td><p>-( x^2 + y^2 ) + (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0</p></td>
|
|
<td><p>A dumbbell</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>ellipsoid</p></td>
|
|
<td><p>a b c</p></td>
|
|
<td><p>(x/a)^2 + (y/b)^2 + (z/c)^2 = 0</p></td>
|
|
<td><p>An ellipsoid</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>gaussian_bump</p></td>
|
|
<td><p>A l rc1 rc2</p></td>
|
|
<td><p>if( x < rc1) -z + A * exp( -x^2 / (2 l^2) ); else if( x < rc2 ) -z + a + b*x + c*x^2 + d*x^3; else z</p></td>
|
|
<td><p>A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0.</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>plane</p></td>
|
|
<td><p>a b c x0 y0 z0</p></td>
|
|
<td><p>a*(x-x0) + b*(y-y0) + c*(z-z0) = 0</p></td>
|
|
<td><p>A plane with normal (a,b,c) going through point (x0,y0,z0)</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>plane_wiggle</p></td>
|
|
<td><p>a w</p></td>
|
|
<td><p>z - a*sin(w*x) = 0</p></td>
|
|
<td><p>A plane with a sinusoidal modulation on z along x.</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>sphere</p></td>
|
|
<td><p>R</p></td>
|
|
<td><p>x^2 + y^2 + z^2 - R^2 = 0</p></td>
|
|
<td><p>A sphere of radius R</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>supersphere</p></td>
|
|
<td><p>R q</p></td>
|
|
<td><p>| x |^q + | y |^q + | z |^q - R^q = 0</p></td>
|
|
<td><p>A supersphere of hyperradius R</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>spine</p></td>
|
|
<td><p>a, A, B, B2, c</p></td>
|
|
<td><p>-(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise</p></td>
|
|
<td><p>An approximation to a dendritic spine</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>spine_two</p></td>
|
|
<td><p>a, A, B, B2, c</p></td>
|
|
<td><p>-(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise</p></td>
|
|
<td><p>Another approximation to a dendritic spine</p></td>
|
|
</tr>
|
|
<tr class="row-odd"><td><p>thylakoid</p></td>
|
|
<td><p>wB LB lB</p></td>
|
|
<td><p>Various, see <a class="reference internal" href="#paquay1"><span class="std std-ref">(Paquay)</span></a></p></td>
|
|
<td><p>A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB</p></td>
|
|
</tr>
|
|
<tr class="row-even"><td><p>torus</p></td>
|
|
<td><p>R r</p></td>
|
|
<td><p>(R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2</p></td>
|
|
<td><p>A torus with large radius R and small radius r, centered on (0,0,0)</p></td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
<p id="paquay1"><strong>(Paquay)</strong> Paquay and Kusters, Biophys. J., 110, 6, (2016).
|
|
preprint available at <a class="reference external" href="https://arxiv.org/abs/1411.3019/">arXiv:1411.3019</a>.</p>
|
|
</section>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
|
|
<a href="Howto_peri.html" class="btn btn-neutral float-left" title="8.5.9. Peridynamics with LAMMPS" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
|
|
<a href="Howto_rheo.html" class="btn btn-neutral float-right" title="8.5.11. Reproducing hydrodynamics and elastic objects (RHEO)" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
|
|
</div>
|
|
|
|
<hr/>
|
|
|
|
<div role="contentinfo">
|
|
<p>© Copyright 2003-2025 Sandia Corporation.</p>
|
|
</div>
|
|
|
|
Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
|
|
<a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
|
|
provided by <a href="https://readthedocs.org">Read the Docs</a>.
|
|
|
|
|
|
</footer>
|
|
</div>
|
|
</div>
|
|
</section>
|
|
</div>
|
|
<script>
|
|
jQuery(function () {
|
|
SphinxRtdTheme.Navigation.enable(false);
|
|
});
|
|
</script>
|
|
|
|
</body>
|
|
</html> |