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<li class="breadcrumb-item active"><span class="section-number">8.2.7. </span>NEMD simulations</li>
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<a href="Howto_dispersion.html" class="btn btn-neutral float-right" title="8.2.8. Long-range dispersion settings" accesskey="n">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="nemd-simulations">
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<h1><span class="section-number">8.2.7. </span>NEMD simulations<a class="headerlink" href="#nemd-simulations" title="Link to this heading"></a></h1>
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<p>Non-equilibrium molecular dynamics or NEMD simulations are typically
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used to measure a fluid’s rheological properties such as viscosity.
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In LAMMPS, such simulations can be performed by first setting up a
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non-orthogonal simulation box (see the preceding Howto section).</p>
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<p>A shear strain can be applied to the simulation box at a desired
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strain rate by using the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> command. The
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<a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">fix nvt/sllod</span></a> command can be used to thermostat
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the sheared fluid and integrate the SLLOD equations of motion for the
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system. Fix nvt/sllod uses <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a> to compute a thermal temperature
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by subtracting out the streaming velocity of the shearing atoms. The
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velocity profile or other properties of the fluid can be monitored via
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the <a class="reference internal" href="fix_ave_chunk.html"><span class="doc">fix ave/chunk</span></a> command.</p>
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<div class="admonition note">
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<p class="admonition-title">Note</p>
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<p>A recent (2017) book by <a class="reference internal" href="#daivis-nemd"><span class="std std-ref">(Daivis and Todd)</span></a>
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discusses use of the SLLOD method and non-equilibrium MD (NEMD)
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thermostatting generally, for both simple and complex fluids,
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e.g. molecular systems. The latter can be tricky to do correctly.</p>
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</div>
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<p>As discussed in the previous section on non-orthogonal simulation
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boxes, the amount of tilt or skew that can be applied is limited by
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LAMMPS for computational efficiency to be 1/2 of the parallel box
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length. However, <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> can continuously strain
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a box by an arbitrary amount. As discussed in the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> command, when the tilt value reaches a limit,
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the box is flipped to the opposite limit which is an equivalent tiling
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of periodic space. The strain rate can then continue to change as
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before. In a long NEMD simulation these box re-shaping events may
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occur many times.</p>
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<p>In a NEMD simulation, the “remap” option of <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> should be set to “remap v”, since that is what
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<a class="reference internal" href="fix_nvt_sllod.html"><span class="doc">fix nvt/sllod</span></a> assumes to generate a velocity
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profile consistent with the applied shear strain rate.</p>
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<p>An alternative method for calculating viscosities is provided via the
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<a class="reference internal" href="fix_viscosity.html"><span class="doc">fix viscosity</span></a> command.</p>
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<p>NEMD simulations can also be used to measure transport properties of a fluid
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through a pore or channel. Simulations of steady-state flow can be performed
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using the <a class="reference internal" href="fix_flow_gauss.html"><span class="doc">fix flow/gauss</span></a> command.</p>
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<hr class="docutils" />
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<p id="daivis-nemd"><strong>(Daivis and Todd)</strong> Daivis and Todd, Nonequilibrium Molecular Dynamics (book),
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Cambridge University Press, <a class="reference external" href="https://doi.org/10.1017/9781139017848">https://doi.org/10.1017/9781139017848</a>, (2017).</p>
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