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<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 &lt;fixID&gt; &lt;group&gt; atc &lt;type&gt; &lt;parameter_file&gt;
</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<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 &quot;temperature&quot;
# 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&#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<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, &#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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