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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<a class="headerlink" href="#fix-langevin-drude-command" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="syntax">
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<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID langevin/drude Tcom damp_com seed_com Tdrude damp_drude seed_drude keyword values ...
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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"><em>fix</em></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<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
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<div class="highlight-python"><div class="highlight"><pre>fix 3 all langevin/drude 300.0 100.0 19377 1.0 20.0 83451
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fix 1 all langevin/drude 298.15 100.0 19377 5.0 10.0 83451 zero yes
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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<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
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<p>Apply two Langevin thermostats as described in <a class="reference internal" href="tutorial_drude.html#jiang"><span>(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"><em>thermalized Drude oscillator model</em></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>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:
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begin{equation} V’ = frac {M, V + m, v} {M’} end{equation}
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begin{equation} v’ = v - V end{equation}
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Masses:
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begin{equation} M’ = M + m end{equation}
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begin{equation} m’ = frac {M, m } {M’} end{equation}
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The Langevin forces are computed as
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begin{equation} F’ = - frac {M’} {mathtt{damp_com}}, V’ + F_r’ end{equation}
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begin{equation} f’ = - frac {m’} {mathtt{damp_drude}}, v’ + f_r’ end{equation}
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(F_r’) is a random force proportional to
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(sqrt { frac {2, k_B mathtt{Tcom}, m’}</p>
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<blockquote>
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<div><blockquote>
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<div>{mathrm dt, mathtt{damp_com} }</div></blockquote>
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<p>} ).</p>
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</div></blockquote>
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<p>(f_r’) is a random force proportional to
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(sqrt { frac {2, k_B mathtt{Tdrude}, m’}</p>
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<blockquote>
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<div><blockquote>
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<div>{mathrm dt, mathtt{damp_drude} }</div></blockquote>
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<p>} ).</p>
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</div></blockquote>
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<p>Then the real forces acting on the particles are computed from the inverse
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transform:
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begin{equation} F = frac M {M’}, F’ - f’ end{equation}
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begin{equation} f = frac m {M’}, F’ + f’ end{equation}</p>
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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 warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">Like the <a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a> command,
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this fix does NOT perform time integration. It only modifies forces to
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effect thermostating. Thus you must use a separate time integration
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fix, like <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> or <a class="reference internal" href="fix_nh.html"><em>fix nph</em></a> to actually
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update the velocities and positions of atoms using the modified
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forces. Likewise, this fix should not normally be used on atoms that
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also have their temperature controlled by another fix - e.g. by <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a> or <a class="reference internal" href="fix_temp_rescale.html"><em>fix temp/rescale</em></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>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"><em>fix drude</em></a> command to
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specify the Drude status of each atom type.</p>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">only the Drude core atoms need to be in the group
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specified for this fix. A Drude electron will be transformed together
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with its cores even if it is not itself in the group. It is safe to
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include Drude electrons or non-polarizable atoms in the group. The
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non-polarizable atoms will simply not be thermostatted as if they had
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a massless Drude partner (electron).</p>
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</div>
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<div class="admonition warning">
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<p class="first admonition-title">Warning</p>
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<p class="last">Ghost atoms need to know their velocity for this fix
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to act correctly. You must use the <a class="reference internal" href="comm_modify.html"><em>comm_modify</em></a>
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command to enable this, e.g.</p>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>comm_modify vel yes
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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"><em>variable</em></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"><em>thermo_style</em></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"><em>compute commands</em></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"><em>fix_modify</em></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"><em>compute commands</em></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"><em>units</em></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 relatice coordinates, respectively, can be
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calculated using the <a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></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-python"><div class="highlight"><pre>comm_modify vel yes
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fix TEMP all langevin/drude 300. 100. 1256 1. 20. 13977 zero yes
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fix NPH ATOMS rigid/nph/small molecule iso 1. 1. 500.
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fix NVE DRUDES nve
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thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TATOM c_TDRUDE f_TEMP[1] f_TEMP[2]
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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</li>
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<li>oscillators will be frozen and the system will lose its</li>
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<li>polarizability. <em>zero yes</em> avoids a drift of the center of mass of</li>
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<li>the system, but is a bit slower. use two different random seeds to</li>
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<li>avoid unphysical correlations. temperature is controlled by the fix</li>
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<li><em>langevin/drude</em>, so the time-integration fixes do not thermostate.</li>
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<li>don’t forget to 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</li>
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<li>particles and <em>nph</em> for atoms/cores (or vice versa). Do not use <em>nph</em></li>
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<li>for both. contrary to the alternative thermostating using Nose-Hoover</li>
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<li>thermostat fix <em>npt</em> and fix <em>drude/transform</em>, the <em>fix_modify</em></li>
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<li>command is not required here, because the fix <em>nph</em> computes the</li>
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<li>global pressure even if its group is <em>ATOMS</em>. This is what we want. If</li>
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<li>we thermostated <em>ATOMS</em> using <em>npt</em>, the pressure should be the global</li>
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<li>one, but the temperature should be only that of the cores. That’s why</li>
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<li>the command <em>fix_modify</em> should be called in that case. f_TEMP[1]</li>
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<li>and f_TEMP[2] contain the reduced temperatures of the cores/atoms</li>
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<li>and of the Drude particles (see below). They should be 300. and 1. on</li>
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<li>average here.</li>
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</ul>
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</div>
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<hr class="docutils" />
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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<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
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<p>No information about this fix is written to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>. Because the state of the random number generator
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is not saved in restart files, this means you cannot do “exact”
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restarts with this fix, where the simulation continues on the same as
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if no restart had taken place. However, in a statistical sense, a
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restarted simulation should produce the same behavior.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> <em>temp</em> option is supported by this
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fix. You can use it to assign a temperature <a class="reference internal" href="compute.html"><em>compute</em></a>
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you have defined to this fix which will be used in its thermostating
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procedure, as described above. For consistency, the group used by the
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compute should include the group of this fix and the Drude particles.</p>
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<p>This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
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<blockquote>
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<div>none</div></blockquote>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
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<p><a class="reference internal" href="fix_langevin.html"><em>fix langevin</em></a>,
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<a class="reference internal" href="fix_drude.html"><em>fix drude</em></a>,
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<a class="reference internal" href="fix_drude_transform.html"><em>fix drude/transform</em></a>,
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<a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></a>,
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<a class="reference internal" href="pair_thole.html"><em>pair_style thole</em></a></p>
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</div>
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<div class="section" id="default">
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<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
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<p>The option defaults are zero = no.</p>
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<hr class="docutils" />
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<p id="jiang"><strong>(Jiang)</strong> Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J
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Phys Chem Lett, 2, 87-92 (2011).</p>
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