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<div class="section" id="fix-nvt-sllod-command">
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<span id="index-0"></span><h1>fix nvt/sllod command</h1>
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</div>
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<div class="section" id="fix-nvt-sllod-intel-command">
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<h1>fix nvt/sllod/intel command</h1>
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</div>
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<div class="section" id="fix-nvt-sllod-omp-command">
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<h1>fix nvt/sllod/omp command</h1>
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<div class="section" id="syntax">
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<h2>Syntax</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">nvt</span><span class="o">/</span><span class="n">sllod</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
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</pre></div>
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</div>
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<ul class="simple">
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<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
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<li>nvt/sllod = style name of this fix command</li>
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<li>additional thermostat related keyword/value pairs from the <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> command can be appended</li>
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</ul>
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</div>
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<div class="section" id="examples">
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<h2>Examples</h2>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nvt</span><span class="o">/</span><span class="n">sllod</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nvt</span><span class="o">/</span><span class="n">sllod</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span> <span class="n">drag</span> <span class="mf">0.2</span>
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</pre></div>
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</div>
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</div>
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<div class="section" id="description">
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<h2>Description</h2>
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<p>Perform constant NVT integration to update positions and velocities
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each timestep for atoms in the group using a Nose/Hoover temperature
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thermostat. V is volume; T is temperature. This creates a system
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trajectory consistent with the canonical ensemble.</p>
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<p>This thermostat is used for a simulation box that is changing size
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and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
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The size/shape change is induced by use of the <a class="reference internal" href="fix_deform.html"><span class="doc">fix deform</span></a> command, so each point in the simulation box
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can be thought of as having a “streaming” velocity. This
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position-dependent streaming velocity is subtracted from each atom’s
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actual velocity to yield a thermal velocity which is used for
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temperature computation and thermostatting. For example, if the box
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is being sheared in x, relative to y, then points at the bottom of the
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box (low y) have a small x velocity, while points at the top of the
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box (hi y) have a large x velocity. These velocities do not
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contribute to the thermal “temperature” of the atom.</p>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last"><a class="reference internal" href="fix_deform.html"><span class="doc">Fix deform</span></a> has an option for remapping either
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atom coordinates or velocities to the changing simulation box. To use
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fix nvt/sllod, fix deform should NOT remap atom positions, because fix
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nvt/sllod adjusts the atom positions and velocities to create a
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velocity profile that matches the changing box size/shape. Fix deform
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SHOULD remap atom velocities when atoms cross periodic boundaries
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since that is consistent with maintaining the velocity profile created
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by fix nvt/sllod. LAMMPS will give an error if this setting is not
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consistent.</p>
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</div>
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<p>The SLLOD equations of motion, originally proposed by Hoover and Ladd
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(see <a class="reference internal" href="#evans"><span class="std std-ref">(Evans and Morriss)</span></a>), were proven to be equivalent to
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Newton’s equations of motion for shear flow by <a class="reference internal" href="#evans"><span class="std std-ref">(Evans and Morriss)</span></a>. They were later shown to generate the desired
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velocity gradient and the correct production of work by stresses for
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all forms of homogeneous flow by <a class="reference internal" href="#daivis"><span class="std std-ref">(Daivis and Todd)</span></a>. As
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implemented in LAMMPS, they are coupled to a Nose/Hoover chain
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thermostat in a velocity Verlet formulation, closely following the
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implementation used for the <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> command.</p>
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<p>Additional parameters affecting the thermostat are specified by
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keywords and values documented with the <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>
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command. See, for example, discussion of the <em>temp</em> and <em>drag</em>
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keywords.</p>
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<p>This fix computes a temperature each timestep. To do this, the fix
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creates its own compute of style “temp/deform”, as if this command had
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been issued:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">deform</span>
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</pre></div>
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</div>
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<p>See the <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a> command for
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details. Note that the ID of the new compute is the fix-ID +
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underscore + “temp”, and the group for the new compute is the same as
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the fix group.</p>
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<p>Note that this is NOT the compute used by thermodynamic output (see
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the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command) with ID = <em>thermo_temp</em>.
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This means you can change the attributes of this fix’s temperature
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(e.g. its degrees-of-freedom) via the
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<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command or print this temperature
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during thermodynamic output via the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command using the appropriate compute-ID.
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It also means that changing attributes of <em>thermo_temp</em> will have no
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effect on this fix.</p>
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<p>Like other fixes that perform thermostatting, this fix can be used
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with <a class="reference internal" href="compute.html"><span class="doc">compute commands</span></a> that calculate a temperature
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after removing a “bias” from the atom velocities. E.g. removing the
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center-of-mass velocity from a group of atoms or only calculating
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temperature on the x-component of velocity or only calculating
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temperature for atoms in a geometric region. This is not done by
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default, but only if the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> command is used
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to assign a temperature compute to this fix that includes such a bias
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term. See the doc pages for individual <a class="reference internal" href="compute.html"><span class="doc">compute commands</span></a> to determine which ones include a bias. In
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this case, the thermostat works in the following manner: the current
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temperature is calculated taking the bias into account, bias is
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removed from each atom, thermostatting is performed on the remaining
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thermal degrees of freedom, and the bias is added back in.</p>
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<hr class="docutils" />
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<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a>
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.</p>
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<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
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<p>You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
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use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
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<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
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more instructions on how to use the accelerated styles effectively.</p>
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</div>
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<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
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<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
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<p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
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command for info on how to re-specify a fix in an input script that
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reads a restart file, so that the operation of the fix continues in an
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uninterrupted fashion.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> option is supported by this
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fix. You can use it to assign a <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> you have
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defined to this fix which will be used in its thermostatting
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procedure.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
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fix to add the energy change induced by Nose/Hoover thermostatting to
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the system’s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
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<p>This fix computes the same global scalar and global vector of
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quantities as does the <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> command.</p>
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<p>This fix can ramp its target temperature over multiple runs, using the
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<em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. See the
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<a class="reference internal" href="run.html"><span class="doc">run</span></a> command for details of how to do this.</p>
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<p>This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<p>This fix works best without Nose-Hoover chain thermostats, i.e. using
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tchain = 1. Setting tchain to larger values can result in poor
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equilibration.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
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<a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a>, <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default</h2>
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<p>Same as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, except tchain = 1.</p>
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<hr class="docutils" />
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<p id="evans"><strong>(Evans and Morriss)</strong> Evans and Morriss, Phys Rev A, 30, 1528 (1984).</p>
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<p id="daivis"><strong>(Daivis and Todd)</strong> Daivis and Todd, J Chem Phys, 124, 194103 (2006).</p>
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