<spanid="index-0"></span><h1>fix drude/transform/direct command<aclass="headerlink"href="#fix-drude-transform-direct-command"title="Permalink to this headline">¶</a></h1>
<h1>fix drude/transform/inverse command<aclass="headerlink"href="#fix-drude-transform-inverse-command"title="Permalink to this headline">¶</a></h1>
<divclass="section"id="syntax">
<h2>Syntax<aclass="headerlink"href="#syntax"title="Permalink to this headline">¶</a></h2>
<divclass="highlight-python"><divclass="highlight"><pre>fix ID group-ID style keyword value ...
</pre></div>
</div>
<ulclass="simple">
<li>ID, group-ID are documented in <aclass="reference internal"href="fix.html"><em>fix</em></a> command</li>
<li>style = <em>drude/transform/direct</em> or <em>drude/transform/inverse</em></li>
</ul>
</div>
<divclass="section"id="examples">
<h2>Examples<aclass="headerlink"href="#examples"title="Permalink to this headline">¶</a></h2>
<divclass="highlight-python"><divclass="highlight"><pre>fix 3 all drude/transform/direct
fix 1 all drude/transform/inverse
</pre></div>
</div>
</div>
<divclass="section"id="description">
<h2>Description<aclass="headerlink"href="#description"title="Permalink to this headline">¶</a></h2>
<p>Transform the coordinates of Drude oscillators from real to reduced
and back for thermalizing the Drude oscillators as described in
<aclass="reference internal"href="tutorial_drude.html#lamoureux"><span>(Lamoureux)</span></a> using a Nose-Hoover thermostat. This fix is
designed to be used with the <aclass="reference internal"href="tutorial_drude.html"><em>thermalized Drude oscillator model</em></a>. Polarizable models in LAMMPS are
described in <aclass="reference internal"href="Section_howto.html#howto-25"><span>this Section</span></a>.</p>
<p>Drude oscillators are a pair of atoms representing a single
polarizable atom. Ideally, the mass of Drude particles would vanish
and their positions would be determined self-consistently by iterative
minimization of the energy, the cores’ positions being fixed. It is
however more efficient and it yields comparable results, if the Drude
oscillators (the motion of the Drude particle relative to the core)
are thermalized at a low temperature. In that case, the Drude
particles need a small mass.</p>
<p>The thermostats act on the reduced degrees of freedom, which are
defined by the following equations. Note that 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>Masses: begin{equation} M’ = M + m end{equation}
begin{equation} m’ = frac {M, m } {M’} end{equation}
Positions: begin{equation} X’ = frac {M, X + m, x} {M’}
end{equation} begin{equation} x’ = x - X end{equation}
Velocities: begin{equation} V’ = frac {M, V + m, v} {M’}
end{equation} begin{equation} v’ = v - V end{equation}
Forces: begin{equation} F’ = F + f end{equation}
begin{equation} f’ = frac { M, f - m, F} {M’}
end{equation}</p>
<p>This transform conserves the total kinetic energy
begin{equation} X, F + x, f = X’, F’ + x’, f’ end{equation}</p>
<hrclass="docutils"/>
<p>This fix requires each atom know whether it is a Drude particle or
not. You must therefore use the <aclass="reference internal"href="fix_drude.html"><em>fix drude</em></a> command to
specify the Drude status of each atom type.</p>
<divclass="admonition warning">
<pclass="first admonition-title">Warning</p>
<pclass="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 not be transformed.</p>
</div>
<hrclass="docutils"/>
<p>This fix does NOT perform time integration. It only transform masses,
coordinates, velocities and forces. Thus you must use separate time
integration fixes, like <aclass="reference internal"href="fix_nve.html"><em>fix nve</em></a> or <aclass="reference internal"href="fix_nh.html"><em>fix npt</em></a> to actually update the velocities and positions of
atoms. In order to thermalize the reduced degrees of freedom at
different temperatures, two Nose-Hoover thermostats must be defined,
acting on two distinct groups.</p>
<divclass="admonition warning">
<pclass="first admonition-title">Warning</p>
<pclass="last">The <em>fix drude/transform/direct</em> command must appear
before any Nose-Hoover thermostating fixes. The <em>fix
drude/transform/inverse</em> command must appear after any Nose-Hoover
thermostating fixes.</p>
</div>
<p>Example:</p>
<divclass="highlight-python"><divclass="highlight"><pre>fix fDIRECT all drude/transform/direct
fix fNVT gCORES nvt temp 300.0 300.0 100.0
fix fNVT gDRUDES nvt temp 1.0 1.0 100.0
fix fINVERSE all drude/transform/inverse
compute TDRUDE all temp/drude
thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
</pre></div>
</div>
<p>In this example, <em>gCORES</em> is the group of the atom cores and <em>gDRUDES</em>
is the group of the Drude particles (electrons). The centers of mass
of the Drude oscillators will be thermostated at 300.0 and the
internal degrees of freedom will be thermostated at 1.0. The
temperatures of cores and Drude particles, in center-of-mass and
relatice coordinates, are calculated using <aclass="reference internal"href="compute_temp_drude.html"><em>compute temp/drude</em></a></p>
<p>In addition, if you want to use a barostat to simulate a system at
constant pressure, only one of the Nose-Hoover fixes must be <em>npt</em>,
the other one should be <em>nvt</em>. You must add a <em>compute temp/com</em> and a
<em>fix_modify</em> command so that the temperature of the <em>npt</em> fix be just
that of its group but the pressure be the overall pressure
<h2>Restart, fix_modify, output, run start/stop, minimize info<aclass="headerlink"href="#restart-fix-modify-output-run-start-stop-minimize-info"title="Permalink to this headline">¶</a></h2>
<p>No information about this fix is written to <aclass="reference internal"href="restart.html"><em>binary restart files</em></a>.</p>
</div>
<divclass="section"id="restrictions">
<h2>Restrictions<aclass="headerlink"href="#restrictions"title="Permalink to this headline">¶</a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<divclass="section"id="related-commands">
<h2>Related commands<aclass="headerlink"href="#related-commands"title="Permalink to this headline">¶</a></h2>
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