<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>
<preclass="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>
<ulclass="simple">
<li>parameter_file = name of the file with material parameters. Note: Neither hardy nor field requires a parameter file</li>
</ul>
</div>
<divclass="section"id="examples">
<h2>Examples</h2>
<preclass="literal-block">
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>
<divclass="section"id="description">
<h2>Description</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-default"><divclass="highlight"><pre><span></span><spanclass="c1"># ... commands to create and initialize the MD system</span>
</pre></div>
</div>
<divclass="highlight-default"><divclass="highlight"><pre><span></span><spanclass="c1"># initial fix to designate post-processing and the group to apply it to</span>
<spanclass="c1"># no material file is allowed nor required</span>
<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>
<hrclass="docutils"/>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<p>No information about this fix is written to <aclass="reference internal"href="restart.html"><spanclass="doc">binary restart files</span></a>. The <aclass="reference internal"href="fix_modify.html"><spanclass="doc">fix_modify</span></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"><spanclass="std std-ref">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"><spanclass="doc">run</span></a> command. This fix is not invoked during <aclass="reference internal"href="minimize.html"><spanclass="doc">energy minimization</span></a>.</p>
</div>
<divclass="section"id="restrictions">
<h2>Restrictions</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</h2>
<p>After specifying this fix in your input script, several other <aclass="reference internal"href="fix_modify.html"><spanclass="doc">fix_modify</span></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</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>
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