<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>
<p>The following coupling example is typical, but non-exhaustive:<br/>
</p>
<p><code> # ... commands to create and initialize the MD system <br/>
</code></p>
<p><code> # initial fix to designate coupling type and group to apply it to <br/>
# tag group physics material_file <br/>
fix AtC internal atc thermal Ar_thermal.mat<br/>
<br/>
# create a uniform 12 x 2 x 2 mesh that covers region contain the group <br/>
# nx ny nz region periodicity <br/>
fix_modify AtC mesh create 12 2 2 mdRegion f p p<br/>
<br/>
# specify the control method for the type of coupling <br/>
# physics control_type <br/>
fix_modify AtC thermal control flux <br/>
<br/>
# specify the initial values for the empirical field "temperature" <br/>
# field node_group value <br/>
fix_modify AtC initial temperature all 30.<br/>
<br/>
# create an output stream for nodal fields <br/>
# filename output_frequency <br/>
fix_modify AtC output atc_fe_output 100<br/>
<br/>
</code></p>
<p><code> run 1000 <br/>
</code></p>
<p>likewise for this post-processing example: <br/>
</p>
<p><code> # ... commands to create and initialize the MD system <br/>
</code></p>
<p><code> # initial fix to designate post-processing and the group to apply it to <br/>
# no material file is allowed nor required <br/>
fix AtC internal atc hardy <br/>
<br/>
# for hardy fix, specific kernel function (function type and range) to # be used as a localization function <br/>
fix AtC kernel quartic_sphere 10.0 <br/>
<br/>
# create a uniform 1 x 1 x 1 mesh that covers region contain the group <br/>
# with periodicity this effectively creats a system average <br/>
fix_modify AtC mesh create 1 1 1 box p p p <br/>
<br/>
# change from default lagrangian map to eulerian <br/>
<li>Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, <em> An atomistic-to-continuum coupling method for heat transfer in solids. </em> Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351. <br/>
</li>
<li>Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, <em> Calculation of stress in atomistic simulation. </em> Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319. <br/>
</li>
<li>Zimmerman, JA; Jones, RE; Templeton, JA, <em> A material frame approach for evaluating continuum variables in atomistic simulations. </em> Journal of Computational Physics (2010), 229:2364. <br/>
</li>
<li>Templeton, JA; Jones, RE; Wagner, GJ, <em> Application of a field-based method to spatially varying thermal transport problems in molecular dynamics. </em> Modelling and Simulation in Materials Science and Engineering (2010), 18:085007. <br/>
</li>
<li>Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, <em> Electron transport enhanced molecular dynamics for metals and semi-metals. </em> International Journal for Numerical Methods in Engineering (2010), 83:940. <br/>
</li>
<li>Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, <em> A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling. </em> Journal of Chemical Theory and Computation (2011), 7:1736. <br/>
</li>
<li>Mandadapu, KK; Templeton, JA; Lee, JW, <em> Polarization as a field variable from molecular dynamics simulations. </em> Journal of Chemical Physics (2013), 139:054115. <br/>
</li>
</ul>
<p>Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes <em> The finite element method </em>, Dover 2003, for the basics of FE simulation.</p>
<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>
<p>Currently,</p>
<ul>
<li>the coupling is restricted to thermal physics</li>
<li>the FE computations are done in serial on each processor.</li>
