forked from lijiext/lammps
434 lines
28 KiB
HTML
434 lines
28 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 atc 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 atc 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-atc-command">
|
|
<span id="index-0"></span><h1>fix atc command<a class="headerlink" href="#fix-atc-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>fix <fixID> <group> atc <type> <parameter_file>
|
|
</pre></div>
|
|
</div>
|
|
<ul class="simple">
|
|
<li>fixID = name of fix</li>
|
|
<li>group = name of group fix is to be applied</li>
|
|
<li>type = <em>thermal</em> or <em>two_temperature</em> or <em>hardy</em> or <em>field</em></li>
|
|
</ul>
|
|
<pre class="literal-block">
|
|
<em>thermal</em> = thermal coupling with fields: temperature
|
|
<em>two_temperature</em> = electron-phonon coupling with field: temperature and electron_temperature
|
|
<em>hardy</em> = on-the-fly post-processing using kernel localization functions (see "related" section for possible fields)
|
|
<em>field</em> = on-the-fly post-processing using mesh-based localization functions (see "related" section for possible fields)
|
|
</pre>
|
|
<ul class="simple">
|
|
<li>parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file</li>
|
|
</ul>
|
|
</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>fix AtC internal atc thermal Ar_thermal.dat
|
|
fix AtC internal atc two_temperature Ar_ttm.mat
|
|
fix AtC internal atc hardy
|
|
fix AtC internal atc field
|
|
</pre></div>
|
|
</div>
|
|
</div>
|
|
<div class="section" id="description">
|
|
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
|
<p>This fix is the beginning to creating a coupled FE/MD simulation and/or an on-the-fly estimation of continuum fields. The coupled versions of this fix do Verlet integration and the post-processing does not. After instantiating this fix, several other fix_modify commands will be needed to set up the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.</p>
|
|
<img alt="_images/atc_nanotube.jpg" class="align-center" src="_images/atc_nanotube.jpg" />
|
|
<div class="highlight-python"><div class="highlight"><pre>The following coupling example is typical, but non-exhaustive:
|
|
# ... commands to create and initialize the MD system
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre># initial fix to designate coupling type and group to apply it to
|
|
# tag group physics material_file
|
|
fix AtC internal atc thermal Ar_thermal.mat
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre># create a uniform 12 x 2 x 2 mesh that covers region contain the group
|
|
# nx ny nz region periodicity
|
|
fix_modify AtC mesh create 12 2 2 mdRegion f p p
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre># specify the control method for the type of coupling
|
|
# physics control_type
|
|
fix_modify AtC thermal control flux
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre># specify the initial values for the empirical field "temperature"
|
|
# field node_group value
|
|
fix_modify AtC initial temperature all 30
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre># create an output stream for nodal fields
|
|
# filename output_frequency
|
|
fix_modify AtC output atc_fe_output 100
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>run 1000
|
|
</pre></div>
|
|
</div>
|
|
<p>likewise for this post-processing example:</p>
|
|
<div class="highlight-python"><div class="highlight"><pre><span class="c"># ... commands to create and initialize the MD system</span>
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre># initial fix to designate post-processing and the group to apply it to
|
|
# no material file is allowed nor required
|
|
fix AtC internal atc hardy
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre># for hardy fix, specific kernel function (function type and range) to # be used as a localization function
|
|
fix AtC kernel quartic_sphere 10.0
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre># create a uniform 1 x 1 x 1 mesh that covers region contain the group
|
|
# with periodicity this effectively creats a system average
|
|
fix_modify AtC mesh create 1 1 1 box p p p
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre># change from default lagrangian map to eulerian
|
|
# refreshed every 100 steps
|
|
fix_modify AtC atom_element_map eulerian 100
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre># start with no field defined
|
|
# add mass density, potential energy density, stress and temperature
|
|
fix_modify AtC fields add density energy stress temperature
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre># create an output stream for nodal fields
|
|
# filename output_frequency
|
|
fix_modify AtC output nvtFE 100 text
|
|
</pre></div>
|
|
</div>
|
|
<div class="highlight-python"><div class="highlight"><pre>run 1000
|
|
</pre></div>
|
|
</div>
|
|
<dl class="docutils">
|
|
<dt>the mesh’s linear interpolation functions can be used as the localization function</dt>
|
|
<dd>by using the field option:</dd>
|
|
</dl>
|
|
<p>fix AtC internal atc field</p>
|
|
<p>fix_modify AtC mesh create 1 1 1 box p p p</p>
|
|
<p>...</p>
|
|
<p>Note coupling and post-processing can be combined in the same simulations using separate fixes.</p>
|
|
</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<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
|
|
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options relevant to this fix are listed below. No global scalar or vector or per-atom quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. No parameter of this fix can be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
|
|
</div>
|
|
<div class="section" id="restrictions">
|
|
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
|
<p>Thermal and two_temperature (coupling) types use a Verlet time-integration algorithm. The hardy type does not contain its own time-integrator and must be used with a separate fix that does contain one, e.g. nve, nvt, etc.</p>
|
|
<ul class="simple">
|
|
<li>Currently,</li>
|
|
<li><ul class="first">
|
|
<li>the coupling is restricted to thermal physics</li>
|
|
</ul>
|
|
</li>
|
|
<li><ul class="first">
|
|
<li>the FE computations are done in serial on each processor.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
|
<p>After specifying this fix in your input script, several other <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> commands are used to setup the problem, e.g. define the finite element mesh and prescribe initial and boundary conditions.</p>
|
|
<p>fix_modify commands for setup:</p>
|
|
<ul class="simple">
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">mesh</span> <span class="pre">create</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">mesh</span> <span class="pre">quadrature</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">mesh</span> <span class="pre">read</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">mesh</span> <span class="pre">write</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">mesh</span> <span class="pre">create_nodeset</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">mesh</span> <span class="pre">add_to_nodeset</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">mesh</span> <span class="pre">create_faceset</span> <span class="pre">box</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">mesh</span> <span class="pre">create_faceset</span> <span class="pre">plane</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">mesh</span> <span class="pre">create_elementset</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">mesh</span> <span class="pre">delete_elements</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">mesh</span> <span class="pre">nodeset_to_elementset</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">boundary</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">internal_quadrature</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">time_integration</span> <span class="pre">(thermal)</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">time_integration</span> <span class="pre">(momentum)</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">extrinsic</span> <span class="pre">electron_integration</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">internal_element_set</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">decomposition</span></code></li>
|
|
</ul>
|
|
<p>fix_modify commands for boundary and initial conditions:</p>
|
|
<ul class="simple">
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">initial</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">fix</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">unfix</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">fix_flux</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">unfix_flux</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">source</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">remove_source</span></code></li>
|
|
</ul>
|
|
<p>fix_modify commands for control and filtering:</p>
|
|
<ul class="simple">
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">control</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">control</span> <span class="pre">thermal</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">control</span> <span class="pre">thermal</span> <span class="pre">correction_max_iterations</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">control</span> <span class="pre">momentum</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">control</span> <span class="pre">localized_lambda</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">control</span> <span class="pre">lumped_lambda_solve</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">control</span> <span class="pre">mask_direction</span></code> control</li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">filter</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">filter</span> <span class="pre">scale</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">filter</span> <span class="pre">type</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">equilibrium_start</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">extrinsic</span> <span class="pre">exchange</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">poisson_solver</span></code></li>
|
|
</ul>
|
|
<p>fix_modify commands for output:</p>
|
|
<ul class="simple">
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">output</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">output</span> <span class="pre">nodeset</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">output</span> <span class="pre">elementset</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">output</span> <span class="pre">boundary_integral</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">output</span> <span class="pre">contour_integral</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">mesh</span> <span class="pre">output</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">write_restart</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">read_restart</span></code></li>
|
|
</ul>
|
|
<p>fix_modify commands for post-processing:</p>
|
|
<ul class="simple">
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">kernel</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">fields</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">grdients</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">rates</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">computes</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">on_the_fly</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">pair_interactions/bond_interactions</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">sample_frequency</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">set</span></code></li>
|
|
</ul>
|
|
<p>miscellaneous fix_modify commands:</p>
|
|
<ul class="simple">
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">atom_element_map</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">atom_weight</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">write_atom_weights</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">reset_time</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">reset_atomic_reference_positions</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">fe_md_boundary</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">boundary_faceset</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">consistent_fe_initialization</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">mass_matrix</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">material</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">atomic_charge</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">source_integration</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">temperature_definition</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">track_displacement</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">boundary_dynamics</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">add_species</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">add_molecule</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">remove_species</span></code></li>
|
|
<li><code class="xref doc docutils literal"><span class="pre">fix_modify</span> <span class="pre">AtC</span> <span class="pre">remove_molecule</span></code></li>
|
|
</ul>
|
|
<p>Note: a set of example input files with the attendant material files are included with this package</p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
|
<p>None</p>
|
|
<hr class="docutils" />
|
|
<p>For detailed exposition of the theory and algorithms please see:</p>
|
|
<p id="wagner"><strong>(Wagner)</strong> Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, “An atomistic-to-continuum coupling method for heat transfer in solids.” Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.</p>
|
|
<p id="zimmeman2004"><strong>(Zimmerman2004)</strong> Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, “Calculation of stress in atomistic simulation.” Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.</p>
|
|
<p id="zimmerman2010"><strong>(Zimmerman2010)</strong> Zimmerman, JA; Jones, RE; Templeton, JA, “A material frame approach for evaluating continuum variables in atomistic simulations.” Journal of Computational Physics (2010), 229:2364.</p>
|
|
<p id="templeton2010"><strong>(Templeton2010)</strong> Templeton, JA; Jones, RE; Wagner, GJ, “Application of a field-based method to spatially varying thermal transport problems in molecular dynamics.” Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.</p>
|
|
<p id="jones"><strong>(Jones)</strong> Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, “Electron transport enhanced molecular dynamics for metals and semi-metals.” International Journal for Numerical Methods in Engineering (2010), 83:940.</p>
|
|
<p id="templeton2011"><strong>(Templeton2011)</strong> Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, “A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling.” Journal of Chemical Theory and Computation (2011), 7:1736.</p>
|
|
<p id="mandadapu"><strong>(Mandadapu)</strong> Mandadapu, KK; Templeton, JA; Lee, JW, “Polarization as a field variable from molecular dynamics simulations.” Journal of Chemical Physics (2013), 139:054115.</p>
|
|
<p>Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes ” The finite element method ”, Dover 2003, for the basics of FE simulation.</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> |