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<div class="section" id="fix-atc-command">
<span id="index-0"></span><h1>fix atc command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="o">&lt;</span><span class="n">fixID</span><span class="o">&gt;</span> <span class="o">&lt;</span><span class="n">group</span><span class="o">&gt;</span> <span class="n">atc</span> <span class="o">&lt;</span><span class="nb">type</span><span class="o">&gt;</span> <span class="o">&lt;</span><span class="n">parameter_file</span><span class="o">&gt;</span>
</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 &quot;related&quot; section for possible fields)
<em>field</em> = on-the-fly post-processing using mesh-based localization functions (see &quot;related&quot; 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</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">thermal</span> <span class="n">Ar_thermal</span><span class="o">.</span><span class="n">dat</span>
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">two_temperature</span> <span class="n">Ar_ttm</span><span class="o">.</span><span class="n">mat</span>
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">hardy</span>
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">field</span>
</pre></div>
</div>
</div>
<div class="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>
<img alt="_images/atc_nanotube.jpg" class="align-center" src="_images/atc_nanotube.jpg" />
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">The</span> <span class="n">following</span> <span class="n">coupling</span> <span class="n">example</span> <span class="ow">is</span> <span class="n">typical</span><span class="p">,</span> <span class="n">but</span> <span class="n">non</span><span class="o">-</span><span class="n">exhaustive</span><span class="p">:</span>
<span class="c1"># ... commands to create and initialize the MD system</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># initial fix to designate coupling type and group to apply it to</span>
<span class="c1"># tag group physics material_file</span>
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">thermal</span> <span class="n">Ar_thermal</span><span class="o">.</span><span class="n">mat</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create a uniform 12 x 2 x 2 mesh that covers region contain the group</span>
<span class="c1"># nx ny nz region periodicity</span>
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">mesh</span> <span class="n">create</span> <span class="mi">12</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">mdRegion</span> <span class="n">f</span> <span class="n">p</span> <span class="n">p</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># specify the control method for the type of coupling</span>
<span class="c1"># physics control_type</span>
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">thermal</span> <span class="n">control</span> <span class="n">flux</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># specify the initial values for the empirical field &quot;temperature&quot;</span>
<span class="c1"># field node_group value</span>
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">initial</span> <span class="n">temperature</span> <span class="nb">all</span> <span class="mi">30</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create an output stream for nodal fields</span>
<span class="c1"># filename output_frequency</span>
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">output</span> <span class="n">atc_fe_output</span> <span class="mi">100</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run</span> <span class="mi">1000</span>
</pre></div>
</div>
<p>likewise for this post-processing example:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># ... commands to create and initialize the MD system</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># initial fix to designate post-processing and the group to apply it to</span>
<span class="c1"># no material file is allowed nor required</span>
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">hardy</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># for hardy fix, specific kernel function (function type and range) to # be used as a localization function</span>
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">kernel</span> <span class="n">quartic_sphere</span> <span class="mf">10.0</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create a uniform 1 x 1 x 1 mesh that covers region contain the group</span>
<span class="c1"># with periodicity this effectively creats a system average</span>
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">mesh</span> <span class="n">create</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">p</span> <span class="n">p</span> <span class="n">p</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># change from default lagrangian map to eulerian</span>
<span class="c1"># refreshed every 100 steps</span>
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">atom_element_map</span> <span class="n">eulerian</span> <span class="mi">100</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># start with no field defined</span>
<span class="c1"># add mass density, potential energy density, stress and temperature</span>
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">fields</span> <span class="n">add</span> <span class="n">density</span> <span class="n">energy</span> <span class="n">stress</span> <span class="n">temperature</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create an output stream for nodal fields</span>
<span class="c1"># filename output_frequency</span>
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">output</span> <span class="n">nvtFE</span> <span class="mi">100</span> <span class="n">text</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run</span> <span class="mi">1000</span>
</pre></div>
</div>
<dl class="docutils">
<dt>the mesh&#8217;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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. The <a class="reference internal" href="fix_modify.html"><span class="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 <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">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"><span class="doc">run</span></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div>
<div class="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>
<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</h2>
<p>After specifying this fix in your input script, several other <a class="reference internal" href="fix_modify.html"><span class="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>fix_modify commands for setup:</p>
<ul class="simple">
<li><a class="reference external" href="USER/atc/man_mesh_create.html">fix_modify AtC mesh create</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_quadrature.html">fix_modify AtC mesh quadrature</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_read.html">fix_modify AtC mesh read</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_write.html">fix_modify AtC mesh write</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_create_nodeset.html">fix_modify AtC mesh create_nodeset</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_add_to_nodeset.html">fix_modify AtC mesh add_to_nodeset</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_create_faceset_box.html">fix_modify AtC mesh create_faceset box</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_create_faceset_plane.html">fix_modify AtC mesh create_faceset plane</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_create_elementset.html">fix_modify AtC mesh create_elementset</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_delete_elements.html">fix_modify AtC mesh delete_elements</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_nodeset_to_elementset.html">fix_modify AtC mesh nodeset_to_elementset</a></li>
<li><a class="reference external" href="USER/atc/man_boundary.html">fix_modify AtC boundary</a></li>
<li><a class="reference external" href="USER/atc/man_internal_quadrature.html">fix_modify AtC internal_quadrature</a></li>
<li><a class="reference external" href="USER/atc/man_thermal_time_integration.html">fix_modify AtC time_integration (thermal)</a></li>
<li><a class="reference external" href="USER/atc/man_momentum_time_integration.html">fix_modify AtC time_integration (momentum)</a></li>
<li><a class="reference external" href="USER/atc/man_electron_integration.html">fix_modify AtC extrinsic electron_integration</a></li>
<li><a class="reference external" href="USER/atc/man_internal_element_set.html">fix_modify AtC internal_element_set</a></li>
<li><a class="reference external" href="USER/atc/man_decomposition.html">fix_modify AtC decomposition</a></li>
</ul>
<p>fix_modify commands for boundary and initial conditions:</p>
<ul class="simple">
<li><a class="reference external" href="USER/atc/man_initial.html">fix_modify AtC initial</a></li>
<li><a class="reference external" href="USER/atc/man_fix_nodes.html">fix_modify AtC fix</a></li>
<li><a class="reference external" href="USER/atc/man_unfix_nodes.html">fix_modify AtC unfix</a></li>
<li><a class="reference external" href="USER/atc/man_fix_flux.html">fix_modify AtC fix_flux</a></li>
<li><a class="reference external" href="USER/atc/man_unfix_flux.html">fix_modify AtC unfix_flux</a></li>
<li><a class="reference external" href="USER/atc/man_source.html">fix_modify AtC source</a></li>
<li><a class="reference external" href="USER/atc/man_remove_source.html">fix_modify AtC remove_source</a></li>
</ul>
<p>fix_modify commands for control and filtering:</p>
<ul class="simple">
<li><a class="reference external" href="USER/atc/man_control.html">fix_modify AtC control</a></li>
<li><a class="reference external" href="USER/atc/man_control_thermal.html">fix_modify AtC control thermal</a></li>
<li><a class="reference external" href="USER/atc/man_control_thermal_correction_max_iterations.html">fix_modify AtC control thermal correction_max_iterations</a></li>
<li><a class="reference external" href="USER/atc/man_control_momentum.html">fix_modify AtC control momentum</a></li>
<li><a class="reference external" href="USER/atc/man_localized_lambda.html">fix_modify AtC control localized_lambda</a></li>
<li><a class="reference external" href="USER/atc/man_lumped_lambda_solve.html">fix_modify AtC control lumped_lambda_solve</a></li>
<li><a class="reference external" href="USER/atc/man_mask_direction.html">fix_modify AtC control mask_direction</a> control</li>
<li><a class="reference external" href="USER/atc/man_time_filter.html">fix_modify AtC filter</a></li>
<li><a class="reference external" href="USER/atc/man_filter_scale.html">fix_modify AtC filter scale</a></li>
<li><a class="reference external" href="USER/atc/man_filter_type.html">fix_modify AtC filter type</a></li>
<li><a class="reference external" href="USER/atc/man_equilibrium_start.html">fix_modify AtC equilibrium_start</a></li>
<li><a class="reference external" href="USER/atc/man_extrinsic_exchange.html">fix_modify AtC extrinsic exchange</a></li>
<li><a class="reference external" href="USER/atc/man_poisson_solver.html">fix_modify AtC poisson_solver</a></li>
</ul>
<p>fix_modify commands for output:</p>
<ul class="simple">
<li><a class="reference external" href="USER/atc/man_output.html">fix_modify AtC output</a></li>
<li><a class="reference external" href="USER/atc/man_output_nodeset.html">fix_modify AtC output nodeset</a></li>
<li><a class="reference external" href="USER/atc/man_output_elementset.html">fix_modify AtC output elementset</a></li>
<li><a class="reference external" href="USER/atc/man_boundary_integral.html">fix_modify AtC output boundary_integral</a></li>
<li><a class="reference external" href="USER/atc/man_contour_integral.html">fix_modify AtC output contour_integral</a></li>
<li><a class="reference external" href="USER/atc/man_mesh_output.html">fix_modify AtC mesh output</a></li>
<li><a class="reference external" href="USER/atc/man_write_restart.html">fix_modify AtC write_restart</a></li>
<li><a class="reference external" href="USER/atc/man_read_restart.html">fix_modify AtC read_restart</a></li>
</ul>
<p>fix_modify commands for post-processing:</p>
<ul class="simple">
<li><a class="reference external" href="USER/atc/man_hardy_kernel.html">fix_modify AtC kernel</a></li>
<li><a class="reference external" href="USER/atc/man_hardy_fields.html">fix_modify AtC fields</a></li>
<li><a class="reference external" href="USER/atc/man_hardy_gradients.html">fix_modify AtC grdients</a></li>
<li><a class="reference external" href="USER/atc/man_hardy_rates.html">fix_modify AtC rates</a></li>
<li><a class="reference external" href="USER/atc/man_hardy_computes.html">fix_modify AtC computes</a></li>
<li><a class="reference external" href="USER/atc/man_hardy_on_the_fly.html">fix_modify AtC on_the_fly</a></li>
<li><a class="reference external" href="USER/atc/man_pair_interactions.html">fix_modify AtC pair_interactions/bond_interactions</a></li>
<li><a class="reference external" href="USER/atc/man_sample_frequency.html">fix_modify AtC sample_frequency</a></li>
<li><a class="reference external" href="USER/atc/man_set.html">fix_modify AtC set</a></li>
</ul>
<p>miscellaneous fix_modify commands:</p>
<ul class="simple">
<li><a class="reference external" href="USER/atc/man_atom_element_map.html">fix_modify AtC atom_element_map</a></li>
<li><a class="reference external" href="USER/atc/man_atom_weight.html">fix_modify AtC atom_weight</a></li>
<li><a class="reference external" href="USER/atc/man_write_atom_weights.html">fix_modify AtC write_atom_weights</a></li>
<li><a class="reference external" href="USER/atc/man_reset_time.html">fix_modify AtC reset_time</a></li>
<li><a class="reference external" href="USER/atc/man_reset_atomic_reference_positions.html">fix_modify AtC reset_atomic_reference_positions</a></li>
<li><a class="reference external" href="USER/atc/man_fe_md_boundary.html">fix_modify AtC fe_md_boundary</a></li>
<li><a class="reference external" href="USER/atc/man_boundary_faceset.html">fix_modify AtC boundary_faceset</a></li>
<li><a class="reference external" href="USER/atc/man_consistent_fe_initialization.html">fix_modify AtC consistent_fe_initialization</a></li>
<li><a class="reference external" href="USER/atc/man_mass_matrix.html">fix_modify AtC mass_matrix</a></li>
<li><a class="reference external" href="USER/atc/man_material.html">fix_modify AtC material</a></li>
<li><a class="reference external" href="USER/atc/man_atomic_charge.html">fix_modify AtC atomic_charge</a></li>
<li><a class="reference external" href="USER/atc/man_source_integration.html">fix_modify AtC source_integration</a></li>
<li><a class="reference external" href="USER/atc/man_temperature_definition.html">fix_modify AtC temperature_definition</a></li>
<li><a class="reference external" href="USER/atc/man_track_displacement.html">fix_modify AtC track_displacement</a></li>
<li><a class="reference external" href="USER/atc/man_boundary_dynamics.html">fix_modify AtC boundary_dynamics</a></li>
<li><a class="reference external" href="USER/atc/man_add_species.html">fix_modify AtC add_species</a></li>
<li><a class="reference external" href="USER/atc/man_add_molecule.html">fix_modify AtC add_molecule</a></li>
<li><a class="reference external" href="USER/atc/man_remove_species.html">fix_modify AtC remove_species</a></li>
<li><a class="reference external" href="USER/atc/man_remove_molecule.html">fix_modify AtC remove_molecule</a></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</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, &#8220;An atomistic-to-continuum coupling method for heat transfer in solids.&#8221; 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, &#8220;Calculation of stress in atomistic simulation.&#8221; 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, &#8220;A material frame approach for evaluating continuum variables in atomistic simulations.&#8221; Journal of Computational Physics (2010), 229:2364.</p>
<p id="templeton2010"><strong>(Templeton2010)</strong> Templeton, JA; Jones, RE; Wagner, GJ, &#8220;Application of a field-based method to spatially varying thermal transport problems in molecular dynamics.&#8221; 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, &#8220;Electron transport enhanced molecular dynamics for metals and semi-metals.&#8221; 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, &#8220;A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling.&#8221; Journal of Chemical Theory and Computation (2011), 7:1736.</p>
<p id="mandadapu"><strong>(Mandadapu)</strong> Mandadapu, KK; Templeton, JA; Lee, JW, &#8220;Polarization as a field variable from molecular dynamics simulations.&#8221; Journal of Chemical Physics (2013), 139:054115.</p>
<p>Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes &#8221; The finite element method &#8221;, Dover 2003, for the basics of FE simulation.</p>
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