<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
thermalizing the reduced degrees of freedom of Drude oscillators.
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
are discussed in <a class="reference internal" href="Section_howto.html#howto-25"><span class="std std-ref">this Section</span></a>.</p>
<p>Drude oscillators are a way to simulate polarizables atoms, by
splitting them into a core and a Drude particle bound by a harmonic
bond. The thermalization works by transforming the particles degrees
of freedom by these equations. In these equations upper case denotes
atomic or center of mass values and lower case denotes Drude particle
or dipole values. Primes denote the transformed (reduced) values,
while bare letters denote the original values.</p>
<p><span class="math">\(F_r'\)</span> is a random force proportional to
<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
Then the real forces acting on the particles are computed from the inverse
transform:</p>
<div class="math">
\[\begin{equation} F = \frac M {M'}\, F' - f' \end{equation}\]</div>
<div class="math">
\[\begin{equation} f = \frac m {M'}\, F' + f' \end{equation}\]</div>
<p>This fix also thermostates non-polarizable atoms in the group at
temperature <em>Tcom</em>, as if they had a massless Drude partner. The
Drude particles themselves need not be in the group. The center of
mass and the dipole are thermostated iff the core atom is in the
group.</p>
<p>Note that the thermostat effect of this fix is applied to only the
translational degrees of freedom of the particles, which is an
important consideration if finite-size particles, which have
rotational degrees of freedom, are being thermostated. The
translational degrees of freedom can also have a bias velocity removed
from them before thermostating takes place; see the description below.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Like the <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> command, this fix does
NOT perform time integration. It only modifies forces to effect
thermostating. Thus you must use a separate time integration fix, like
<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
velocities and positions of atoms using the modified forces.
Likewise, this fix should not normally be used on atoms that also have
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>
</div>
<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
a discussion of different ways to compute temperature and perform
thermostating.</p>
<hr class="docutils" />
<p>This fix requires each atom know whether it is a Drude particle or
not. You must therefore use the <a class="reference internal" href="fix_drude.html"><span class="doc">fix drude</span></a> command to
specify the Drude status of each atom type.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">only the Drude core atoms need to be in the group specified for
this fix. A Drude electron will be transformed together with its cores
even if it is not itself in the group. It is safe to include Drude
electrons or non-polarizable atoms in the group. The non-polarizable
atoms will simply be thermostatted as if they had a massless Drude
partner (electron).</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Ghost atoms need to know their velocity for this fix to act
correctly. You must use the <a class="reference internal" href="comm_modify.html"><span class="doc">comm_modify</span></a> command to
<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>
Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.