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<li>fix langevin/drude command</li>
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<div class="section" id="fix-langevin-drude-command">
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<span id="index-0"></span><h1>fix langevin/drude 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">langevin</span><span class="o">/</span><span class="n">drude</span> <span class="n">Tcom</span> <span class="n">damp_com</span> <span class="n">seed_com</span> <span class="n">Tdrude</span> <span class="n">damp_drude</span> <span class="n">seed_drude</span> <span class="n">keyword</span> <span class="n">values</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>langevin/drude = style name of this fix command</li>
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<li>Tcom = desired temperature of the centers of mass (temperature units)</li>
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<li>damp_com = damping parameter for the thermostat on centers of mass (time units)</li>
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<li>seed_com = random number seed to use for white noise of the thermostat on centers of mass (positive integer)</li>
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<li>Tdrude = desired temperature of the Drude oscillators (temperature units)</li>
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<li>damp_drude = damping parameter for the thermostat on Drude oscillators (time units)</li>
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<li>seed_drude = random number seed to use for white noise of the thermostat on Drude oscillators (positive integer)</li>
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<li>zero or more keyword/value pairs may be appended</li>
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<li>keyword = <em>zero</em></li>
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</ul>
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<pre class="literal-block">
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<em>zero</em> value = <em>no</em> or <em>yes</em>
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<em>no</em> = do not set total random force on centers of mass to zero
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<em>yes</em> = set total random force on centers of mass to zero
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</pre>
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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">3</span> <span class="nb">all</span> <span class="n">langevin</span><span class="o">/</span><span class="n">drude</span> <span class="mf">300.0</span> <span class="mf">100.0</span> <span class="mi">19377</span> <span class="mf">1.0</span> <span class="mf">20.0</span> <span class="mi">83451</span>
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<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">langevin</span><span class="o">/</span><span class="n">drude</span> <span class="mf">298.15</span> <span class="mf">100.0</span> <span class="mi">19377</span> <span class="mf">5.0</span> <span class="mf">10.0</span> <span class="mi">83451</span> <span class="n">zero</span> <span class="n">yes</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>Apply two Langevin thermostats as described in <a class="reference internal" href="tutorial_drude.html#jiang"><span class="std std-ref">(Jiang)</span></a> for
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thermalizing the reduced degrees of freedom of Drude oscillators.
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This link describes how to use the <a class="reference internal" href="tutorial_drude.html"><span class="doc">thermalized Drude oscillator model</span></a> in LAMMPS and polarizable models in LAMMPS
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are discussed in <a class="reference internal" href="Section_howto.html#howto-25"><span class="std std-ref">this Section</span></a>.</p>
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<p>Drude oscillators are a way to simulate polarizables atoms, by
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splitting them into a core and a Drude particle bound by a harmonic
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bond. The thermalization works by transforming the particles degrees
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of freedom by these equations. In these equations upper case denotes
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atomic or center of mass values and lower case denotes Drude particle
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or dipole values. Primes denote the transformed (reduced) values,
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while bare letters denote the original values.</p>
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<p>Velocities:</p>
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<div class="math">
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\[\begin{equation} V' = \frac {M\, V + m\, v} {M'} \end{equation}\]</div>
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<div class="math">
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\[\begin{equation} v' = v - V \end{equation}\]</div>
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<p>Masses:</p>
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<div class="math">
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\[\begin{equation} M' = M + m \end{equation}\]</div>
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<div class="math">
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\[\begin{equation} m' = \frac {M\, m } {M'} \end{equation}\]</div>
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<p>The Langevin forces are computed as</p>
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<div class="math">
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\[\begin{equation} F' = - \frac {M'} {\mathtt{damp\_com}}\, V' + F_r' \end{equation}\]</div>
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<div class="math">
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\[\begin{equation} f' = - \frac {m'} {\mathtt{damp\_drude}}\, v' + f_r' \end{equation}\]</div>
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<p><span class="math">\(F_r'\)</span> is a random force proportional to
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<span class="math">\(\sqrt { \frac {2\, k_B \mathtt{Tcom}\, m'} {\mathrm dt\, \mathtt{damp\_com} } }\)</span>. <a href="#id1"><span class="problematic" id="id2">:b:math:`f_r’`</span></a> is a random force proportional to
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<span class="math">\(\sqrt { \frac {2\, k_B \mathtt{Tdrude}\, m'} {\mathrm dt\, \mathtt{damp\_drude} } }\)</span>.
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Then the real forces acting on the particles are computed from the inverse
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transform:</p>
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<div class="math">
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\[\begin{equation} F = \frac M {M'}\, F' - f' \end{equation}\]</div>
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<div class="math">
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\[\begin{equation} f = \frac m {M'}\, F' + f' \end{equation}\]</div>
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<p>This fix also thermostates non-polarizable atoms in the group at
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temperature <em>Tcom</em>, as if they had a massless Drude partner. The
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Drude particles themselves need not be in the group. The center of
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mass and the dipole are thermostated iff the core atom is in the
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group.</p>
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<p>Note that the thermostat effect of this fix is applied to only the
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translational degrees of freedom of the particles, which is an
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important consideration if finite-size particles, which have
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rotational degrees of freedom, are being thermostated. The
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translational degrees of freedom can also have a bias velocity removed
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from them before thermostating takes place; see the description below.</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">Like the <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> command, this fix does
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NOT perform time integration. It only modifies forces to effect
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thermostating. Thus you must use a separate time integration fix, like
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<a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> or <a class="reference internal" href="fix_nh.html"><span class="doc">fix nph</span></a> to actually update the
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velocities and positions of atoms using the modified forces.
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Likewise, this fix should not normally be used on atoms that also have
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their temperature controlled by another fix - e.g. by <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a> commands.</p>
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</div>
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<p>See <a class="reference internal" href="Section_howto.html#howto-16"><span class="std std-ref">this howto section</span></a> of the manual for
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a discussion of different ways to compute temperature and perform
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thermostating.</p>
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<hr class="docutils" />
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<p>This fix requires each atom know whether it is a Drude particle or
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not. You must therefore use the <a class="reference internal" href="fix_drude.html"><span class="doc">fix drude</span></a> command to
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specify the Drude status of each atom type.</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">only the Drude core atoms need to be in the group specified for
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this fix. A Drude electron will be transformed together with its cores
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even if it is not itself in the group. It is safe to include Drude
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electrons or non-polarizable atoms in the group. The non-polarizable
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atoms will simply be thermostatted as if they had a massless Drude
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partner (electron).</p>
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</div>
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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">Ghost atoms need to know their velocity for this fix to act
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correctly. You must use the <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify</span></a> command to
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enable this, e.g.</p>
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</div>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_modify</span> <span class="n">vel</span> <span class="n">yes</span>
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</pre></div>
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</div>
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<hr class="docutils" />
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<p><em>Tcom</em> is the target temperature of the centers of mass, which would
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be used to thermostate the non-polarizable atoms. <em>Tdrude</em> is the
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(normally low) target temperature of the core-Drude particle pairs
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(dipoles). <em>Tcom</em> and <em>Tdrude</em> can be specified as an equal-style
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<a class="reference internal" href="variable.html"><span class="doc">variable</span></a>. If the value is a variable, it should be
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specified as v_name, where name is the variable name. In this case,
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the variable will be evaluated each timestep, and its value used to
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determine the target temperature.</p>
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<p>Equal-style variables can specify formulas with various mathematical
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functions, and include <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command
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keywords for the simulation box parameters and timestep and elapsed
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time. Thus it is easy to specify a time-dependent temperature.</p>
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<p>Like other fixes that perform thermostating, this fix can be used with
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<a class="reference internal" href="compute.html"><span class="doc">compute commands</span></a> that remove a “bias” from the atom
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velocities. E.g. removing the center-of-mass velocity from a group of
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atoms. This is not done by default, but only if the
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<a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> command is used to assign a temperature
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compute to this fix that includes such a bias term. See the doc pages
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for individual <a class="reference internal" href="compute.html"><span class="doc">compute commands</span></a> to determine which ones
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include a bias. In this case, the thermostat works in the following
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manner: bias is removed from each atom, thermostating is performed on
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the remaining thermal degrees of freedom, and the bias is added back
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in. NOTE: this feature has not been tested.</p>
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<p>Note: The temperature thermostating the core-Drude particle pairs
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should be chosen low enough, so as to mimic as closely as possible the
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self-consistent minimization. It must however be high enough, so that
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the dipoles can follow the local electric field exerted by the
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neighbouring atoms. The optimal value probably depends on the
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temperature of the centers of mass and on the mass of the Drude
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particles.</p>
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<p><em>damp_com</em> is the characteristic time for reaching thermal equilibrium
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of the centers of mass. For example, a value of 100.0 means to relax
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the temperature of the centers of mass in a timespan of (roughly) 100
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time units (tau or fmsec or psec - see the <a class="reference internal" href="units.html"><span class="doc">units</span></a>
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command). <em>damp_drude</em> is the characteristic time for reaching
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thermal equilibrium of the dipoles. It is typically a few timesteps.</p>
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<p>The number <em>seed_com</em> and <em>seed_drude</em> are positive integers. They set
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the seeds of the Marsaglia random number generators used for
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generating the random forces on centers of mass and on the
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dipoles. Each processor uses the input seed to generate its own unique
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seed and its own stream of random numbers. Thus the dynamics of the
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system will not be identical on two runs on different numbers of
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processors.</p>
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<p>The keyword <em>zero</em> can be used to eliminate drift due to the
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thermostat on centers of mass. Because the random forces on different
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centers of mass are independent, they do not sum exactly to zero. As
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a result, this fix applies a small random force to the entire system,
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and the momentum of the total center of mass of the system undergoes a
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slow random walk. If the keyword <em>zero</em> is set to <em>yes</em>, the total
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random force on the centers of mass is set exactly to zero by
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subtracting off an equal part of it from each center of mass in the
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group. As a result, the total center of mass of a system with zero
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initial momentum will not drift over time.</p>
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<p>The actual temperatures of cores and Drude particles, in
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center-of-mass and relative coordinates, respectively, can be
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calculated using the <a class="reference internal" href="compute_temp_drude.html"><span class="doc">compute temp/drude</span></a>
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command.</p>
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<hr class="docutils" />
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<p>Usage example for rigid bodies in the NPT ensemble:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">comm_modify</span> <span class="n">vel</span> <span class="n">yes</span>
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<span class="n">fix</span> <span class="n">TEMP</span> <span class="nb">all</span> <span class="n">langevin</span><span class="o">/</span><span class="n">drude</span> <span class="mf">300.</span> <span class="mf">100.</span> <span class="mi">1256</span> <span class="mf">1.</span> <span class="mf">20.</span> <span class="mi">13977</span> <span class="n">zero</span> <span class="n">yes</span>
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<span class="n">fix</span> <span class="n">NPH</span> <span class="n">ATOMS</span> <span class="n">rigid</span><span class="o">/</span><span class="n">nph</span><span class="o">/</span><span class="n">small</span> <span class="n">molecule</span> <span class="n">iso</span> <span class="mf">1.</span> <span class="mf">1.</span> <span class="mf">500.</span>
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<span class="n">fix</span> <span class="n">NVE</span> <span class="n">DRUDES</span> <span class="n">nve</span>
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<span class="n">compute</span> <span class="n">TDRUDE</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">drude</span>
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<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">cpu</span> <span class="n">etotal</span> <span class="n">ke</span> <span class="n">pe</span> <span class="n">ebond</span> <span class="n">ecoul</span> <span class="n">elong</span> <span class="n">press</span> <span class="n">vol</span> <span class="n">temp</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
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</pre></div>
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</div>
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<p>Comments:</p>
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<ul class="simple">
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<li>Drude particles should not be in the rigid group, otherwise the Drude
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oscillators will be frozen and the system will lose its
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polarizability.</li>
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<li><em>zero yes</em> avoids a drift of the center of mass of
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the system, but is a bit slower.</li>
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<li>Use two different random seeds to avoid unphysical correlations.</li>
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<li>Temperature is controlled by the fix <em>langevin/drude</em>, so the
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time-integration fixes do not thermostate. Don’t forget to
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time-integrate both cores and Drude particles.</li>
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<li>Pressure is time-integrated only once by using <em>nve</em> for Drude
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particles and <em>nph</em> for atoms/cores (or vice versa). Do not use <em>nph</em>
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for both.</li>
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<li>The temperatures of cores and Drude particles are calculated by
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<a class="reference internal" href="compute_temp_drude.html"><span class="doc">compute temp/drude</span></a></li>
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<li>Contrary to the alternative thermostating using Nose-Hoover thermostat
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fix <em>npt</em> and <a class="reference internal" href="fix_drude_transform.html"><span class="doc">fix drude/transform</span></a>, the
|
|
<em>fix_modify</em> command is not required here, because the fix <em>nph</em>
|
|
computes the global pressure even if its group is <em>ATOMS</em>. This is
|
|
what we want. If we thermostated <em>ATOMS</em> using <em>npt</em>, the pressure
|
|
should be the global one, but the temperature should be only that of
|
|
the cores. That’s why the command <em>fix_modify</em> should be called in
|
|
that case.</li>
|
|
</ul>
|
|
</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>. Because the state of the random number generator
|
|
is not saved in restart files, this means you cannot do “exact”
|
|
restarts with this fix, where the simulation continues on the same as
|
|
if no restart had taken place. However, in a statistical sense, a
|
|
restarted simulation should produce the same behavior.</p>
|
|
<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
|
|
fix. You can use it to assign a temperature <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>
|
|
you have defined to this fix which will be used in its thermostating
|
|
procedure, as described above. For consistency, the group used by the
|
|
compute should include the group of this fix and the Drude particles.</p>
|
|
<p>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>
|
|
<blockquote>
|
|
<div>none</div></blockquote>
|
|
</div>
|
|
<div class="section" id="related-commands">
|
|
<h2>Related commands</h2>
|
|
<p><a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>,
|
|
<a class="reference internal" href="fix_drude.html"><span class="doc">fix drude</span></a>,
|
|
<a class="reference internal" href="fix_drude_transform.html"><span class="doc">fix drude/transform</span></a>,
|
|
<a class="reference internal" href="compute_temp_drude.html"><span class="doc">compute temp/drude</span></a>,
|
|
<a class="reference internal" href="pair_thole.html"><span class="doc">pair_style thole</span></a></p>
|
|
</div>
|
|
<div class="section" id="default">
|
|
<h2>Default</h2>
|
|
<p>The option defaults are zero = no.</p>
|
|
<hr class="docutils" />
|
|
<p id="jiang"><strong>(Jiang)</strong> Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J
|
|
Phys Chem Lett, 2, 87-92 (2011).</p>
|
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