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<div class="section" id="fix-drude-transform-direct-command">
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<span id="index-0"></span><h1>fix drude/transform/direct command<a class="headerlink" href="#fix-drude-transform-direct-command" title="Permalink to this headline">¶</a></h1>
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</div>
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<div class="section" id="fix-drude-transform-inverse-command">
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<h1>fix drude/transform/inverse command<a class="headerlink" href="#fix-drude-transform-inverse-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 style keyword value ...
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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>style = <em>drude/transform/direct</em> or <em>drude/transform/inverse</em></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<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 drude/transform/direct
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fix 1 all drude/transform/inverse
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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>Transform the coordinates of Drude oscillators from real to reduced
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and back for thermalizing the Drude oscillators as described in
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<a class="reference internal" href="tutorial_drude.html#lamoureux"><span>(Lamoureux)</span></a> using a Nose-Hoover thermostat. This fix is
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designed to be used with the <a class="reference internal" href="tutorial_drude.html"><em>thermalized Drude oscillator model</em></a>. Polarizable models in LAMMPS are
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described 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 pair of atoms representing a single
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polarizable atom. Ideally, the mass of Drude particles would vanish
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and their positions would be determined self-consistently by iterative
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minimization of the energy, the cores’ positions being fixed. It is
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however more efficient and it yields comparable results, if the Drude
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oscillators (the motion of the Drude particle relative to the core)
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are thermalized at a low temperature. In that case, the Drude
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particles need a small mass.</p>
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<p>The thermostats act on the reduced degrees of freedom, which are
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defined by the following equations. Note that in these equations
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upper case denotes atomic or center of mass values and lower case
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denotes Drude particle or dipole values. Primes denote the transformed
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(reduced) values, while bare letters denote the original values.</p>
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<p>Masses: begin{equation} M’ = M + m end{equation}
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begin{equation} m’ = frac {M, m } {M’} end{equation}
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Positions: begin{equation} X’ = frac {M, X + m, x} {M’}
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end{equation} begin{equation} x’ = x - X end{equation}
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Velocities: begin{equation} V’ = frac {M, V + m, v} {M’}
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end{equation} begin{equation} v’ = v - V end{equation}
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Forces: begin{equation} F’ = F + f end{equation}
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begin{equation} f’ = frac { M, f - m, F} {M’}
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end{equation}</p>
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<p>This transform conserves the total kinetic energy
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begin{equation} frac 1 2 , (M, V^2+ m, v^2)
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= frac 1 2 , (M’, V’^2+ m’, v’^2) end{equation}
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and the virial defined with absolute positions
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begin{equation} X, F + x, f = X’, F’ + x’, f’ end{equation}</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 transformed.</p>
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</div>
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<hr class="docutils" />
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<p>This fix does NOT perform time integration. It only transform masses,
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coordinates, velocities and forces. Thus you must use separate time
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integration fixes, 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 npt</em></a> to actually update the velocities and positions of
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atoms. In order to thermalize the reduced degrees of freedom at
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different temperatures, two Nose-Hoover thermostats must be defined,
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acting on two distinct groups.</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">The <em>fix drude/transform/direct</em> command must appear
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before any Nose-Hoover thermostating fixes. The <em>fix
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drude/transform/inverse</em> command must appear after any Nose-Hoover
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thermostating fixes.</p>
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</div>
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<p>Example:</p>
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<div class="highlight-python"><div class="highlight"><pre>fix fDIRECT all drude/transform/direct
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fix fNVT gCORES nvt temp 300.0 300.0 100.0
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fix fNVT gDRUDES nvt temp 1.0 1.0 100.0
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fix fINVERSE all drude/transform/inverse
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compute TDRUDE all temp/drude
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thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
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</pre></div>
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</div>
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<p>In this example, <em>gCORES</em> is the group of the atom cores and <em>gDRUDES</em>
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is the group of the Drude particles (electrons). The centers of mass
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of the Drude oscillators will be thermostated at 300.0 and the
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internal degrees of freedom will be thermostated at 1.0. The
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temperatures of cores and Drude particles, in center-of-mass and
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relatice coordinates, are calculated using <a class="reference internal" href="compute_temp_drude.html"><em>compute temp/drude</em></a></p>
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<p>In addition, if you want to use a barostat to simulate a system at
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constant pressure, only one of the Nose-Hoover fixes must be <em>npt</em>,
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the other one should be <em>nvt</em>. You must add a <em>compute temp/com</em> and a
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<em>fix_modify</em> command so that the temperature of the <em>npt</em> fix be just
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that of its group but the pressure be the overall pressure
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<em>thermo_press</em>.</p>
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<p>Example:</p>
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<div class="highlight-python"><div class="highlight"><pre>compute cTEMP_CORE gCORES temp/com
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fix fDIRECT all drude/transform/direct
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fix fNPT gCORES npt temp 298.0 298.0 100.0 iso 1.0 1.0 500.0
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fix_modify fNPT temp cTEMP_CORE press thermo_press
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fix fNVT gDRUDES nvt temp 5.0 5.0 100.0
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fix fINVERSE all drude/transform/inverse
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</pre></div>
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</div>
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<p>In this example, <em>gCORES</em> is the group of the atom cores and <em>gDRUDES</em>
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is the group of the Drude particles. The centers of mass of the Drude
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oscillators will be thermostated at 298.0 and the internal degrees of
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freedom will be thermostated at 5.0. The whole system will be
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barostated at 1.0.</p>
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<p>In order to avoid the flying ice cube problem (irreversible transfer
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of linear momentum to the center of mass of the system), you may need
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to add a <em>fix momentum</em> command like such as</p>
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<div class="highlight-python"><div class="highlight"><pre>fix fMOMENTUM all momentum 100 linear 1 1 1
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</pre></div>
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</div>
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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>.</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_drude.html"><em>fix drude</em></a>,
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<a class="reference internal" href="fix_langevin_drude.html"><em>fix langevin/drude</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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<p><strong>Default:</strong> none</p>
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<hr class="docutils" />
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<p id="lamoureux"><strong>(Lamoureux)</strong> Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003).</p>
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