2016-05-11 04:05:15 +08:00
<!DOCTYPE html>
<!-- [if IE 8]><html class="no - js lt - ie9" lang="en" > <![endif] -->
<!-- [if gt IE 8]><! --> < html class = "no-js" lang = "en" > <!-- <![endif] -->
< head >
< meta charset = "utf-8" >
< meta name = "viewport" content = "width=device-width, initial-scale=1.0" >
2016-07-31 00:09:11 +08:00
< title > Manifolds (surfacse) — LAMMPS documentation< / title >
2016-05-11 04:05:15 +08:00
< link rel = "stylesheet" href = "_static/css/theme.css" type = "text/css" / >
< link rel = "stylesheet" href = "_static/sphinxcontrib-images/LightBox2/lightbox2/css/lightbox.css" type = "text/css" / >
< link rel = "top" title = "LAMMPS documentation" href = "index.html" / >
< script src = "_static/js/modernizr.min.js" > < / script >
< / head >
< body class = "wy-body-for-nav" role = "document" >
< div class = "wy-grid-for-nav" >
< nav data-toggle = "wy-nav-shift" class = "wy-nav-side" >
< div class = "wy-side-nav-search" >
< a href = "Manual.html" class = "icon icon-home" > LAMMPS
< / a >
< div role = "search" >
< form id = "rtd-search-form" class = "wy-form" action = "search.html" method = "get" >
< input type = "text" name = "q" placeholder = "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 = "main navigation" >
< ul >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_intro.html" > 1. Introduction< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_start.html" > 2. Getting Started< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_commands.html" > 3. Commands< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_packages.html" > 4. Packages< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_accelerate.html" > 5. Accelerating LAMMPS performance< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_howto.html" > 6. How-to discussions< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_example.html" > 7. Example problems< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_perf.html" > 8. Performance & scalability< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_tools.html" > 9. Additional tools< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_modify.html" > 10. Modifying & extending LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_python.html" > 11. Python interface to LAMMPS< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_errors.html" > 12. Errors< / a > < / li >
< li class = "toctree-l1" > < a class = "reference internal" href = "Section_history.html" > 13. Future and history< / a > < / li >
< / ul >
< / div >
< / nav >
< section data-toggle = "wy-nav-shift" class = "wy-nav-content-wrap" >
< nav class = "wy-nav-top" role = "navigation" aria-label = "top navigation" >
< 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" >
< div role = "navigation" aria-label = "breadcrumbs navigation" >
< ul class = "wy-breadcrumbs" >
< li > < a href = "Manual.html" > Docs< / a > » < / li >
2016-07-31 00:09:11 +08:00
< li > Manifolds (surfacse)< / li >
2016-05-11 04:05:15 +08:00
< li class = "wy-breadcrumbs-aside" >
< a href = "http://lammps.sandia.gov" > Website< / a >
< a href = "Section_commands.html#comm" > Commands< / a >
< / li >
< / ul >
< hr / >
< / div >
< div role = "main" class = "document" itemscope = "itemscope" itemtype = "http://schema.org/Article" >
< div itemprop = "articleBody" >
2016-07-31 00:09:11 +08:00
< div class = "section" id = "manifolds-surfacse" >
< h1 > Manifolds (surfacse)< / h1 >
< p > < strong > Overview:< / strong > < / p >
< p > This doc page is not about a LAMMPS input script command, but about
manifolds, which are generalized surfaces, as defined and used by the
USER-MANIFOLD package, to track particle motion on the manifolds. See
the src/USER-MANIFOLD/README file for more details about the package
and its commands.< / p >
< p > Below is a list of currently supported manifolds by the USER-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 >
2016-05-11 04:05:15 +08:00
< table border = "1" class = "docutils" >
< colgroup >
< col width = "5%" / >
< col width = "6%" / >
< col width = "43%" / >
< col width = "46%" / >
< col width = "1%" / >
< / colgroup >
< tbody valign = "top" >
< tr class = "row-odd" > < td > < em > manifold< / em > < / td >
< td > < em > parameters< / em > < / td >
< td > < em > equation< / em > < / td >
< td > < em > description< / em > < / td >
< td > < / td >
< / tr >
< tr class = "row-even" > < td > cylinder< / td >
< td > R< / td >
< td > x^2 + y^2 - R^2 = 0< / td >
< td > Cylinder along z-axis, axis going through (0,0,0)< / td >
< td > < / td >
< / tr >
< tr class = "row-odd" > < td > cylinder_dent< / td >
< td > R l a< / td >
< td > x^2 + y^2 - r(z)^2 = 0, r(x) = R if < a href = "#id7" > < span class = "problematic" id = "id8" > |z|< / span > < / a > > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise< / td >
< td > A cylinder with a dent around z = 0< / td >
< td > < / td >
< / tr >
< tr class = "row-even" > < td > dumbbell< / td >
< td > a A B c< / td >
< td > -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0< / td >
< td > A dumbbell< / td >
< td > < / td >
< / tr >
< tr class = "row-odd" > < td > ellipsoid< / td >
< td > a b c< / td >
< td > (x/a)^2 + (y/b)^2 + (z/c)^2 = 0< / td >
< td > An ellipsoid< / td >
< td > < / td >
< / tr >
< tr class = "row-even" > < td > plane< / td >
< td > a b c x0 y0 z0< / td >
< td > a*(x-x0) + b*(y-y0) + c*(z-z0) = 0< / td >
< td > A plane with normal (a,b,c) going through point (x0,y0,z0)< / td >
< td > < / td >
< / tr >
< tr class = "row-odd" > < td > plane_wiggle< / td >
< td > a w< / td >
< td > z - a*sin(w*x) = 0< / td >
< td > A plane with a sinusoidal modulation on z along x.< / td >
< td > < / td >
< / tr >
< tr class = "row-even" > < td > sphere< / td >
< td > R< / td >
< td > x^2 + y^2 + z^2 - R^2 = 0< / td >
< td > A sphere of radius R< / td >
< td > < / td >
< / tr >
< tr class = "row-odd" > < td > supersphere< / td >
< td > R q< / td >
< td > < a href = "#id1" > < span class = "problematic" id = "id2" > |< / span > < / a > x|^q + < a href = "#id3" > < span class = "problematic" id = "id4" > |< / span > < / a > y|^q + < a href = "#id5" > < span class = "problematic" id = "id6" > |< / span > < / a > z|^q - R^q = 0< / td >
< td > A supersphere of hyperradius R< / td >
< td > < / td >
< / tr >
< tr class = "row-even" > < td > spine< / td >
< td > a, A, B, B2, c< / td >
< td > -(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< / td >
< td > An approximation to a dendtritic spine< / td >
< td > < / td >
< / tr >
< tr class = "row-odd" > < td > spine_two< / td >
< td > a, A, B, B2, c< / td >
< td > -(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< / td >
< td > Another approximation to a dendtritic spine< / td >
< td > < / td >
< / tr >
< tr class = "row-even" > < td > thylakoid< / td >
< td > wB LB lB< / td >
< td > Various, see < a class = "reference internal" href = "#paquay" > < span class = "std std-ref" > (Paquay)< / span > < / a > < / td >
< td > A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB< / td >
< td > < / td >
< / tr >
< tr class = "row-odd" > < td > torus< / td >
< td > R r< / td >
< td > (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2< / td >
< td > A torus with large radius R and small radius r, centered on (0,0,0)< / td >
< td > < / td >
< / tr >
< / tbody >
< / table >
< p id = "paquay" > < strong > (Paquay)< / strong > Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
preprint available at < a class = "reference external" href = "http://arxiv.org/abs/1411.3019/" > arXiv:1411.3019< / a > .< / p >
< / div >
< / div >
< / div >
< footer >
< hr / >
< div role = "contentinfo" >
< p >
© Copyright 2013 Sandia Corporation.
< / p >
< / div >
Built with < a href = "http://sphinx-doc.org/" > Sphinx< / a > using a < a href = "https://github.com/snide/sphinx_rtd_theme" > theme< / a > provided by < a href = "https://readthedocs.org" > Read the Docs< / a > .
< / footer >
< / div >
< / div >
< / section >
< / div >
< script type = "text/javascript" >
var DOCUMENTATION_OPTIONS = {
URL_ROOT:'./',
VERSION:'',
COLLAPSE_INDEX:false,
FILE_SUFFIX:'.html',
HAS_SOURCE: true
};
< / script >
< script type = "text/javascript" src = "_static/jquery.js" > < / script >
< script type = "text/javascript" src = "_static/underscore.js" > < / script >
< script type = "text/javascript" src = "_static/doctools.js" > < / script >
< script type = "text/javascript" src = "https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML" > < / script >
< script type = "text/javascript" src = "_static/sphinxcontrib-images/LightBox2/lightbox2/js/jquery-1.11.0.min.js" > < / script >
< script type = "text/javascript" src = "_static/sphinxcontrib-images/LightBox2/lightbox2/js/lightbox.min.js" > < / script >
< script type = "text/javascript" src = "_static/sphinxcontrib-images/LightBox2/lightbox2-customize/jquery-noconflict.js" > < / script >
< script type = "text/javascript" src = "_static/js/theme.js" > < / script >
< script type = "text/javascript" >
jQuery(function () {
SphinxRtdTheme.StickyNav.enable();
});
< / script >
< / body >
< / html >
