<h2>Description<aclass="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>
<divclass="highlight-python"><divclass="highlight"><pre><spanclass="c"># ... commands to create and initialize the MD system</span>
</pre></div>
</div>
<divclass="highlight-python"><divclass="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>
<divclass="highlight-python"><divclass="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>
<divclass="highlight-python"><divclass="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>
<divclass="highlight-python"><divclass="highlight"><pre># change from default lagrangian map to eulerian
# refreshed every 100 steps
fix_modify AtC atom_element_map eulerian 100
</pre></div>
</div>
<divclass="highlight-python"><divclass="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>
<divclass="highlight-python"><divclass="highlight"><pre># create an output stream for nodal fields
<h2>Restart, fix_modify, output, run start/stop, minimize info<aclass="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 <aclass="reference internal"href="restart.html"><em>binary restart files</em></a>. The <aclass="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 <aclass="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 <aclass="reference internal"href="run.html"><em>run</em></a> command. This fix is not invoked during <aclass="reference internal"href="minimize.html"><em>energy minimization</em></a>.</p>
</div>
<divclass="section"id="restrictions">
<h2>Restrictions<aclass="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>
<ulclass="simple">
<li>Currently,</li>
<li><ulclass="first">
<li>the coupling is restricted to thermal physics</li>
</ul>
</li>
<li><ulclass="first">
<li>the FE computations are done in serial on each processor.</li>
</ul>
</li>
</ul>
</div>
<divclass="section"id="related-commands">
<h2>Related commands<aclass="headerlink"href="#related-commands"title="Permalink to this headline">¶</a></h2>
<p>After specifying this fix in your input script, several other <aclass="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>Note: a set of example input files with the attendant material files are included with this package</p>
</div>
<divclass="section"id="default">
<h2>Default<aclass="headerlink"href="#default"title="Permalink to this headline">¶</a></h2>
<p>None</p>
<hrclass="docutils"/>
<p>For detailed exposition of the theory and algorithms please see:</p>
<pid="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>
<pid="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>
<pid="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>
<pid="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>
<pid="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>
<pid="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>
<pid="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>
Built with <ahref="http://sphinx-doc.org/">Sphinx</a> using a <ahref="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <ahref="https://readthedocs.org">Read the Docs</a>.