forked from lijiext/lammps
307 lines
13 KiB
HTML
307 lines
13 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>compute ti command — LAMMPS 15 May 2015 version 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 15 May 2015 version 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>compute ti 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="compute-ti-command">
|
|
<span id="index-0"></span><h1>compute ti command<a class="headerlink" href="#compute-ti-command" title="Permalink to this headline">¶</a></h1>
|
|
<div class="section" id="syntax">
|
|
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
|
|
<div class="highlight-python"><div class="highlight"><pre>compute ID group ti keyword args ...
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><em>compute</em></a> command</li>
|
|
<li>ti = style name of this compute command</li>
|
|
<li>one or more attribute/arg pairs may be appended</li>
|
|
<li>keyword = pair style (lj/cut, gauss, born, etc) or <em>tail</em> or <em>kspace</em></li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
pair style args = atype v_name1 v_name2
|
|
atype = atom type (see asterisk form below)
|
|
v_name1 = variable with name1 that is energy scale factor and function of lambda
|
|
v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
|
|
<em>tail</em> args = atype v_name1 v_name2
|
|
atype = atom type (see asterisk form below)
|
|
v_name1 = variable with name1 that is energy tail correction scale factor and function of lambda
|
|
v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
|
|
<em>kspace</em> args = atype v_name1 v_name2
|
|
atype = atom type (see asterisk form below)
|
|
v_name1 = variable with name1 that is K-Space scale factor and function of lambda
|
|
v_name2 = variable with name2 that is derivative of v_name1 with respect to lambda
|
|
</pre>
|
|
</div>
|
|
<div class="section" id="examples">
|
|
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
|
<div class="highlight-python"><div class="highlight"><pre>compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
|
|
compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
|
<p>Define a computation that calculates the derivative of the interaction
|
|
potential with respect to <em>lambda</em>, the coupling parameter used in a
|
|
thermodynamic integration. This derivative can be used to infer a
|
|
free energy difference resulting from an alchemical simulation, as
|
|
described in <a class="reference internal" href="#eike"><span>Eike</span></a>.</p>
|
|
<p>Typically this compute will be used in conjunction with the <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a> command which can perform alchemical
|
|
transformations by adusting the strength of an interaction potential
|
|
as a simulation runs, as defined by one or more
|
|
<a class="reference internal" href="pair_style.html"><em>pair_style</em></a> or <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a>
|
|
commands. This scaling is done via a prefactor on the energy, forces,
|
|
virial calculated by the pair or K-Space style. The prefactor is
|
|
often a function of a <em>lambda</em> parameter which may be adjusted from 0
|
|
to 1 (or vice versa) over the course of a <a class="reference internal" href="run.html"><em>run</em></a>. The
|
|
time-dependent adjustment is what the <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a>
|
|
command does.</p>
|
|
<p>Assume that the unscaled energy of a pair_style or kspace_style is
|
|
given by U. Then the scaled energy is</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>Us = f(lambda) U
|
|
</pre></div>
|
|
</div>
|
|
<p>where f() is some function of lambda. What this compute calculates is</p>
|
|
<div class="highlight-python"><div class="highlight"><pre>dUs / d(lambda) = U df(lambda)/dlambda = Us / f(lambda) df(lambda)/dlambda
|
|
</pre></div>
|
|
</div>
|
|
<p>which is the derivative of the system’s scaled potential energy Us
|
|
with respect to <em>lambda</em>.</p>
|
|
<p>To perform this calculation, you provide one or more atom types as
|
|
<em>atype</em>. <em>Atype</em> can be specified in one of two ways. An explicit
|
|
numeric values can be used, as in the 1st example above. Or a
|
|
wildcard asterisk can be used in place of or in conjunction with the
|
|
<em>atype</em> argument to select multiple atom types. This takes the form
|
|
“*” or “<em>n” or “n</em>” or “m*n”. If N = the number of atom types, then
|
|
an asterisk with no numeric values means all types from 1 to N. A
|
|
leading asterisk means all types from 1 to n (inclusive). A trailing
|
|
asterisk means all types from n to N (inclusive). A middle asterisk
|
|
means all types from m to n (inclusive).</p>
|
|
<p>You also specify two functions, as <a class="reference internal" href="variable.html"><em>equal-style variables</em></a>. The first is specified as <em>v_name1</em>, where
|
|
<em>name1</em> is the name of the variable, and is f(lambda) in the notation
|
|
above. The second is specified as <em>v_name2</em>, where <em>name2</em> is the
|
|
name of the variable, and is df(lambda) / dlambda in the notation
|
|
above. I.e. it is the analytic derivative of f() with respect to
|
|
lambda. Note that the <em>name1</em> variable is also typically given as an
|
|
argument to the <a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a> command.</p>
|
|
<p>An alchemical simulation may use several pair potentials together,
|
|
invoked via the <a class="reference internal" href="pair_hybrid.html"><em>pair_style hybrid or hybrid/overlay</em></a>
|
|
command. The total dUs/dlambda for the overall system is calculated
|
|
as the sum of each contributing term as listed by the keywords in the
|
|
compute ti command. Individual pair potentials can be listed, which
|
|
will be sub-styles in the hybrid case. You can also include a K-space
|
|
term via the <em>kspace</em> keyword. You can also include a pairwise
|
|
long-range tail correction to the energy via the <em>tail</em> keyword.</p>
|
|
<p>For each term you can specify a different (or the same) scale factor
|
|
by the two variables that you list. Again, these will typically
|
|
correspond toe the scale factors applied to these various potentials
|
|
and the K-Space contribution via the <a class="reference internal" href="fix_adapt.html"><em>fix_adapt</em></a>
|
|
command.</p>
|
|
<p>More details about the exact functional forms for the computation of
|
|
du/dl can be found in the paper by <a class="reference internal" href="#eike"><span>Eike</span></a>.</p>
|
|
<hr class="docutils" />
|
|
<p><strong>Output info:</strong></p>
|
|
<p>This compute calculates a global scalar, namely dUs/dlambda. This
|
|
value can be used by any command that uses a global scalar value from
|
|
a compute as input. See <a class="reference internal" href="Section_howto.html#howto-15"><span>Section_howto 15</span></a> for an overview of LAMMPS output
|
|
options.</p>
|
|
<p>The scalar value calculated by this compute is “extensive”.</p>
|
|
<p>The scalar value will be in energy <a class="reference internal" href="units.html"><em>units</em></a>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
|
<p>This compute is part of the MISC package. It is only enabled if
|
|
LAMMPS was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p><a class="reference internal" href="fix_adapt.html"><em>fix adapt</em></a></p>
|
|
<p><strong>Default:</strong> none</p>
|
|
<hr class="docutils" />
|
|
<p id="eike"><strong>(Eike)</strong> Eike and Maginn, Journal of Chemical Physics, 124, 164503 (2006).</p>
|
|
</div>
|
|
</div>
|
|
|
|
|
|
</div>
|
|
</div>
|
|
<footer>
|
|
|
|
|
|
<hr/>
|
|
|
|
<div role="contentinfo">
|
|
<p>
|
|
© Copyright .
|
|
</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:'15 May 2015 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> |