forked from lijiext/lammps
471 lines
26 KiB
HTML
471 lines
26 KiB
HTML
|
|
|
|
<!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">
|
|
|
|
<title>fix wall/lj93 command — LAMMPS documentation</title>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<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>
|
|
|
|
<li>fix wall/lj93 command</li>
|
|
<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">
|
|
|
|
<div class="section" id="fix-wall-lj93-command">
|
|
<span id="index-0"></span><h1>fix wall/lj93 command</h1>
|
|
</div>
|
|
<div class="section" id="fix-wall-lj126-command">
|
|
<h1>fix wall/lj126 command</h1>
|
|
</div>
|
|
<div class="section" id="fix-wall-lj1043-command">
|
|
<h1>fix wall/lj1043 command</h1>
|
|
</div>
|
|
<div class="section" id="fix-wall-colloid-command">
|
|
<h1>fix wall/colloid command</h1>
|
|
</div>
|
|
<div class="section" id="fix-wall-harmonic-command">
|
|
<h1>fix wall/harmonic command</h1>
|
|
<div class="section" id="syntax">
|
|
<h2>Syntax</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style</span> <span class="n">face</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
|
|
<li>style = <em>wall/lj93</em> or <em>wall/lj126</em> or <em>wall/lj1043</em> or <em>wall/colloid</em> or <em>wall/harmonic</em></li>
|
|
<li>one or more face/arg pairs may be appended</li>
|
|
<li>face = <em>xlo</em> or <em>xhi</em> or <em>ylo</em> or <em>yhi</em> or <em>zlo</em> or <em>zhi</em></li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
args = coord epsilon sigma cutoff
|
|
coord = position of wall = EDGE or constant or variable
|
|
EDGE = current lo or hi edge of simulation box
|
|
constant = number like 0.0 or -30.0 (distance units)
|
|
variable = <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> like v_x or v_wiggle
|
|
epsilon = strength factor for wall-particle interaction (energy or energy/distance^2 units)
|
|
epsilon can be a variable (see below)
|
|
sigma = size factor for wall-particle interaction (distance units)
|
|
sigma can be a variable (see below)
|
|
cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
|
|
</pre>
|
|
<ul class="simple">
|
|
<li>zero or more keyword/value pairs may be appended</li>
|
|
<li>keyword = <em>units</em> or <em>fld</em></li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
<em>units</em> value = <em>lattice</em> or <em>box</em>
|
|
<em>lattice</em> = the wall position is defined in lattice units
|
|
<em>box</em> = the wall position is defined in simulation box units
|
|
<em>fld</em> value = <em>yes</em> or <em>no</em>
|
|
<em>yes</em> = invoke the wall constraint to be compatible with implicit FLD
|
|
<em>no</em> = invoke the wall constraint in the normal way
|
|
<em>pbc</em> value = <em>yes</em> or <em>no</em>
|
|
<em>yes</em> = allow periodic boundary in a wall dimension
|
|
<em>no</em> = require non-perioidic boundaries in any wall dimension
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples</h2>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">wallhi</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">lj93</span> <span class="n">xlo</span> <span class="o">-</span><span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="n">units</span> <span class="n">box</span>
|
|
<span class="n">fix</span> <span class="n">wallhi</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">lj93</span> <span class="n">xhi</span> <span class="n">EDGE</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
|
|
<span class="n">fix</span> <span class="n">wallhi</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">lj126</span> <span class="n">v_wiggle</span> <span class="mf">23.2</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
|
|
<span class="n">fix</span> <span class="n">zwalls</span> <span class="nb">all</span> <span class="n">wall</span><span class="o">/</span><span class="n">colloid</span> <span class="n">zlo</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.858</span> <span class="n">zhi</span> <span class="mf">40.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.858</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description</h2>
|
|
<p>Bound the simulation domain on one or more of its faces with a flat
|
|
wall that interacts with the atoms in the group by generating a force
|
|
on the atom in a direction perpendicular to the wall. The energy of
|
|
wall-particle interactions depends on the style.</p>
|
|
<p>For style <em>wall/lj93</em>, the energy E is given by the 9/3 potential:</p>
|
|
<img alt="_images/fix_wall_lj93.jpg" class="align-center" src="_images/fix_wall_lj93.jpg" />
|
|
<p>For style <em>wall/lj126</em>, the energy E is given by the 12/6 potential:</p>
|
|
<img alt="_images/pair_lj.jpg" class="align-center" src="_images/pair_lj.jpg" />
|
|
<p>For style <em>wall/lj1043</em>, the energy E is given by the 10/4/3 potential:</p>
|
|
<img alt="_images/fix_wall_lj1043.jpg" class="align-center" src="_images/fix_wall_lj1043.jpg" />
|
|
<p>For style <em>wall/colloid</em>, the energy E is given by an integrated form
|
|
of the <a class="reference internal" href="pair_colloid.html"><span class="doc">pair_style colloid</span></a> potential:</p>
|
|
<img alt="_images/fix_wall_colloid.jpg" class="align-center" src="_images/fix_wall_colloid.jpg" />
|
|
<p>For style <em>wall/harmonic</em>, the energy E is given by a harmonic spring
|
|
potential:</p>
|
|
<img alt="_images/fix_wall_harmonic.jpg" class="align-center" src="_images/fix_wall_harmonic.jpg" />
|
|
<p>In all cases, <em>r</em> is the distance from the particle to the wall at
|
|
position <em>coord</em>, and Rc is the <em>cutoff</em> distance at which the
|
|
particle and wall no longer interact. The energy of the wall
|
|
potential is shifted so that the wall-particle interaction energy is
|
|
0.0 at the cutoff distance.</p>
|
|
<p>Up to 6 walls or faces can be specified in a single command: <em>xlo</em>,
|
|
<em>xhi</em>, <em>ylo</em>, <em>yhi</em>, <em>zlo</em>, <em>zhi</em>. A <em>lo</em> face interacts with
|
|
particles near the lower side of the simulation box in that dimension.
|
|
A <em>hi</em> face interacts with particles near the upper side of the
|
|
simulation box in that dimension.</p>
|
|
<p>The position of each wall can be specified in one of 3 ways: as the
|
|
EDGE of the simulation box, as a constant value, or as a variable. If
|
|
EDGE is used, then the corresponding boundary of the current
|
|
simulation box is used. If a numeric constant is specified then the
|
|
wall is placed at that position in the appropriate dimension (x, y, or
|
|
z). In both the EDGE and constant cases, the wall will never move.
|
|
If the wall position is a variable, it should be specified as v_name,
|
|
where name is an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a> name. In this
|
|
case the variable is evaluated each timestep and the result becomes
|
|
the current position of the reflecting wall. Equal-style variables
|
|
can specify formulas with various mathematical functions, and include
|
|
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command keywords for the simulation
|
|
box parameters and timestep and elapsed time. Thus it is easy to
|
|
specify a time-dependent wall position. See examples below.</p>
|
|
<p>For the <em>wall/lj93</em> and <em>wall/lj126</em> and <em>wall/lj1043</em> styles,
|
|
<em>epsilon</em> and <em>sigma</em> are the usual Lennard-Jones parameters, which
|
|
determine the strength and size of the particle as it interacts with
|
|
the wall. Epsilon has energy units. Note that this <em>epsilon</em> and
|
|
<em>sigma</em> may be different than any <em>epsilon</em> or <em>sigma</em> values defined
|
|
for a pair style that computes particle-particle interactions.</p>
|
|
<p>The <em>wall/lj93</em> interaction is derived by integrating over a 3d
|
|
half-lattice of Lennard-Jones 12/6 particles. The <em>wall/lj126</em>
|
|
interaction is effectively a harder, more repulsive wall interaction.
|
|
The <em>wall/lj1043</em> interaction is yet a different form of wall
|
|
interaction, described in Magda et al in <a class="reference internal" href="#magda"><span class="std std-ref">(Magda)</span></a>.</p>
|
|
<p>For the <em>wall/colloid</em> style, <em>R</em> is the radius of the colloid
|
|
particle, <em>D</em> is the distance from the surface of the colloid particle
|
|
to the wall (r-R), and <em>sigma</em> is the size of a constituent LJ
|
|
particle inside the colloid particle and wall. Note that the cutoff
|
|
distance Rc in this case is the distance from the colloid particle
|
|
center to the wall. The prefactor <em>epsilon</em> can be thought of as an
|
|
effective Hamaker constant with energy units for the strength of the
|
|
colloid-wall interaction. More specifically, the <em>epsilon</em> pre-factor
|
|
= 4 * pi^2 * rho_wall * rho_colloid * epsilon * sigma^6, where epsilon
|
|
and sigma are the LJ parameters for the constituent LJ
|
|
particles. Rho_wall and rho_colloid are the number density of the
|
|
constituent particles, in the wall and colloid respectively, in units
|
|
of 1/volume.</p>
|
|
<p>The <em>wall/colloid</em> interaction is derived by integrating over
|
|
constituent LJ particles of size <em>sigma</em> within the colloid particle
|
|
and a 3d half-lattice of Lennard-Jones 12/6 particles of size <em>sigma</em>
|
|
in the wall. As mentioned in the preceeding paragraph, the density of
|
|
particles in the wall and colloid can be different, as specified by
|
|
the <em>epsilon</em> pre-factor.</p>
|
|
<p>For the <em>wall/harmonic</em> style, <em>epsilon</em> is effectively the spring
|
|
constant K, and has units (energy/distance^2). The input parameter
|
|
<em>sigma</em> is ignored. The minimum energy position of the harmonic
|
|
spring is at the <em>cutoff</em>. This is a repulsive-only spring since the
|
|
interaction is truncated at the <em>cutoff</em></p>
|
|
<p>For any wall, the <em>epsilon</em> and/or <em>sigma</em> parameter can be specified
|
|
as an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>, in which case it should be
|
|
specified as v_name, where name is the variable name. As with a
|
|
variable wall position, the variable is evaluated each timestep and
|
|
the result becomes the current epsilon or sigma of the wall.
|
|
Equal-style variables can specify formulas with various mathematical
|
|
functions, and include <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command
|
|
keywords for the simulation box parameters and timestep and elapsed
|
|
time. Thus it is easy to specify a time-dependent wall interaction.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">For all of the styles, you must insure that r is always > 0 for
|
|
all particles in the group, or LAMMPS will generate an error. This
|
|
means you cannot start your simulation with particles at the wall
|
|
position <em>coord</em> (r = 0) or with particles on the wrong side of the
|
|
wall (r < 0). For the <em>wall/lj93</em> and <em>wall/lj126</em> styles, the energy
|
|
of the wall/particle interaction (and hence the force on the particle)
|
|
blows up as r -> 0. The <em>wall/colloid</em> style is even more
|
|
restrictive, since the energy blows up as D = r-R -> 0. This means
|
|
the finite-size particles of radius R must be a distance larger than R
|
|
from the wall position <em>coord</em>. The <em>harmonic</em> style is a softer
|
|
potential and does not blow up as r -> 0, but you must use a large
|
|
enough <em>epsilon</em> that particles always reamin on the correct side of
|
|
the wall (r > 0).</p>
|
|
</div>
|
|
<p>The <em>units</em> keyword determines the meaning of the distance units used
|
|
to define a wall position, but only when a numeric constant or
|
|
variable is used. It is not relevant when EDGE is used to specify a
|
|
face position. In the variable case, the variable is assumed to
|
|
produce a value compatible with the <em>units</em> setting you specify.</p>
|
|
<p>A <em>box</em> value selects standard distance units as defined by the
|
|
<a class="reference internal" href="units.html"><span class="doc">units</span></a> command, e.g. Angstroms for units = real or metal.
|
|
A <em>lattice</em> value means the distance units are in lattice spacings.
|
|
The <a class="reference internal" href="lattice.html"><span class="doc">lattice</span></a> command must have been previously used to
|
|
define the lattice spacings.</p>
|
|
<p>The <em>fld</em> keyword can be used with a <em>yes</em> setting to invoke the wall
|
|
constraint before pairwise interactions are computed. This allows an
|
|
implicit FLD model using <a class="reference internal" href="pair_lubricateU.html"><span class="doc">pair_style lubricateU</span></a>
|
|
to include the wall force in its calculations. If the setting is
|
|
<em>no</em>, wall forces are imposed after pairwise interactions, in the
|
|
usual manner.</p>
|
|
<p>The <em>pbc</em> keyword can be used with a <em>yes</em> setting to allow walls to
|
|
be specified in a periodic dimension. See the
|
|
<a class="reference internal" href="boundary.html"><span class="doc">boundary</span></a> command for options on simulation box
|
|
boundaries. The default for <em>pbc</em> is <em>no</em>, which means the system
|
|
must be non-periodic when using a wall. But you may wish to use a
|
|
periodic box. E.g. to allow some particles to interact with the wall
|
|
via the fix group-ID, and others to pass through it and wrap around a
|
|
periodic box. In this case you should insure that the wall if
|
|
sufficiently far enough away from the box boundary. If you do not,
|
|
then particles may interact with both the wall and with periodic
|
|
images on the other side of the box, which is probably not what you
|
|
want.</p>
|
|
<hr class="docutils" />
|
|
<p>Here are examples of variable definitions that move the wall position
|
|
in a time-dependent fashion using equal-style
|
|
<a class="reference internal" href="variable.html"><span class="doc">variables</span></a>. The wall interaction parameters (epsilon,
|
|
sigma) could be varied with additional variable definitions.</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">ramp</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
|
|
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_ramp</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">linear</span> <span class="n">equal</span> <span class="n">vdisplace</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="mi">20</span><span class="p">)</span>
|
|
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_linear</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">swiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
|
|
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_wiggle</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">wiggle</span> <span class="n">equal</span> <span class="n">cwiggle</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="mf">5.0</span><span class="p">,</span><span class="mf">3.0</span><span class="p">)</span>
|
|
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">wall</span> <span class="n">xlo</span> <span class="n">v_wiggle</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>The ramp(lo,hi) function adjusts the wall position linearly from lo to
|
|
hi over the course of a run. The vdisplace(c0,velocity) function does
|
|
something similar using the equation position = c0 + velocity*delta,
|
|
where delta is the elapsed time.</p>
|
|
<p>The swiggle(c0,A,period) function causes the wall position to
|
|
oscillate sinusoidally according to this equation, where omega = 2 PI
|
|
/ period:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">)</span>
|
|
</pre></div>
|
|
</div>
|
|
<p>The cwiggle(c0,A,period) function causes the wall position to
|
|
oscillate sinusoidally according to this equation, which will have an
|
|
initial wall velocity of 0.0, and thus may impose a gentler
|
|
perturbation on the particles:</p>
|
|
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">position</span> <span class="o">=</span> <span class="n">c0</span> <span class="o">+</span> <span class="n">A</span> <span class="p">(</span><span class="mi">1</span> <span class="o">-</span> <span class="n">cos</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">))</span>
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<hr class="docutils" />
|
|
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
|
|
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
|
|
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
|
|
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
|
|
fix to add the energy of interaction between atoms and each wall to
|
|
the system’s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
|
|
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
|
|
fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>
|
|
integrator the fix is adding its forces. Default is the outermost level.</p>
|
|
<p>This fix computes a global scalar energy and a global vector of
|
|
forces, which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. Note that the scalar energy is
|
|
the sum of interactions with all defined walls. If you want the
|
|
energy on a per-wall basis, you need to use multiple fix wall
|
|
commands. The length of the vector is equal to the number of walls
|
|
defined by the fix. Each vector value is the normal force on a
|
|
specific wall. Note that an outward force on a wall will be a
|
|
negative value for <em>lo</em> walls and a positive value for <em>hi</em> walls.
|
|
The scalar and vector values calculated by this fix are “extensive”.</p>
|
|
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
|
|
the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>
|
|
<p>The forces due to this fix are imposed during an energy minimization,
|
|
invoked by the <a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command.</p>
|
|
<div class="admonition note">
|
|
<p class="first admonition-title">Note</p>
|
|
<p class="last">If you want the atom/wall interaction energy to be included in
|
|
the total potential energy of the system (the quantity being
|
|
minimized), you MUST enable the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em>
|
|
option for this fix.</p>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions</h2>
|
|
<blockquote>
|
|
<div>none</div></blockquote>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="fix_wall_reflect.html"><span class="doc">fix wall/reflect</span></a>,
|
|
<a class="reference internal" href="fix_wall_gran.html"><span class="doc">fix wall/gran</span></a>,
|
|
<a class="reference internal" href="fix_wall_region.html"><span class="doc">fix wall/region</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults units = lattice, fld = no, and pbc = no.</p>
|
|
<hr class="docutils" />
|
|
<p id="magda"><strong>(Magda)</strong> Magda, Tirrell, Davis, J Chem Phys, 83, 1888-1901 (1985);
|
|
erratum in JCP 84, 2901 (1986).</p>
|
|
</div>
|
|
</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> |