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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<div class="section" id="fix-gle-command">
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<span id="index-0"></span><h1>fix gle 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="nb">id</span><span class="o">-</span><span class="n">group</span> <span class="n">gle</span> <span class="n">Ns</span> <span class="n">Tstart</span> <span class="n">Tstop</span> <span class="n">seed</span> <span class="n">Amatrix</span> <span class="p">[</span><span class="n">noneq</span> <span class="n">Cmatrix</span><span class="p">]</span> <span class="p">[</span><span class="n">every</span> <span class="n">stride</span><span class="p">]</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>gle = style name of this fix command</li>
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<li>Ns = number of additional fictitious momenta</li>
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<li>Tstart, Tstop = temperature ramp during the run</li>
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<li>Amatrix = file to read the drift matrix A from</li>
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<li>seed = random number seed to use for generating noise (positive integer)</li>
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<li>zero or more keyword/value pairs may be appended</li>
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</ul>
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<dl class="docutils">
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<dt>keyword = <em>noneq</em> and/or <em>every</em></dt>
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<dd><p class="first"><em>noneq</em> Cmatrix = file to read the non-equilibrium covariance matrix from
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<em>every</em> stride = apply the GLE once every time steps. Reduces the accuracy</p>
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<blockquote class="last">
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<div>of the integration of the GLE, but has <em>no effect</em> on the accuracy of equilibrium
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sampling. It might change sampling properties when used together with <em>noneq</em>.</div></blockquote>
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</dd>
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</dl>
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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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<p>fix 3 boundary gle 6 300 300 31415 smart.A
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fix 1 all gle 6 300 300 31415 qt-300k.A noneq qt-300k.C</p>
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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 a Generalized Langevin Equation (GLE) thermostat as described
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in <a class="reference internal" href="#ceriotti"><span class="std std-ref">(Ceriotti)</span></a>. The formalism allows one to obtain a number
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of different effects ranging from efficient sampling of all
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vibrational modes in the system to inexpensive (approximate)
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modelling of nuclear quantum effects. Contrary to
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<a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, this fix performs both
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thermostatting and evolution of the Hamiltonian equations of motion, so it
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should not be used together with <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> – at least not
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on the same atom groups.</p>
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<p>Each degree of freedom in the thermostatted group is supplemented
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with Ns additional degrees of freedom s, and the equations of motion
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become</p>
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<p>dq/dt=p/m
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d(p,s)/dt=(F,0) - A(p,s) + B dW/dt</p>
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<p>where F is the physical force, A is the drift matrix (that generalizes
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the friction in Langevin dynamics), B is the diffusion term and dW/dt
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un-correlated Gaussian random forces. The A matrix couples the physical
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(q,p) dynamics with that of the additional degrees of freedom,
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and makes it possible to obtain effectively a history-dependent
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noise and friction kernel.</p>
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<p>The drift matrix should be given as an external file <em>Afile</em>,
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as a (Ns+1 x Ns+1) matrix in inverse time units. Matrices that are
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optimal for a given application and the system of choice can be
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obtained from <a class="reference internal" href="#gle4md"><span class="std std-ref">(GLE4MD)</span></a>.</p>
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<p>Equilibrium sampling a temperature T is obtained by specifiying the
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target value as the <em>Tstart</em> and <em>Tstop</em> arguments, so that the diffusion
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matrix that gives canonical sampling for a given A is computed automatically.
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However, the GLE framework also allow for non-equilibrium sampling, that
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can be used for instance to model inexpensively zero-point energy
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effects <a class="reference internal" href="#ceriotti2"><span class="std std-ref">(Ceriotti2)</span></a>. This is achieved specifying the
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<em>noneq</em> keyword followed by the name of the file that contains the
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static covariance matrix for the non-equilibrium dynamics.</p>
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<p>Since integrating GLE dynamics can be costly when used together with
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simple potentials, one can use the <em>every</em> optional keyword to
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apply the Langevin terms only once every several MD steps, in a
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multiple time-step fashion. This should be used with care when doing
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non-equilibrium sampling, but should have no effect on equilibrium
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averages when using canonical sampling.</p>
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<p>The random number <em>seed</em> must be a positive integer. A Marsaglia random
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number generator is used. Each processor uses the input seed to
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generate its own unique seed and its own stream of random numbers.
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Thus the dynamics of the system will not be identical on two runs on
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different numbers of processors.</p>
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<p>Note also that the Generalized Langevin Dynamics scheme that is
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implemented by the <a class="reference internal" href="fix_gld.html"><span class="doc">fix gld</span></a> scheme is closely related
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to the present one. In fact, it should be always possible to cast the
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Prony series form of the memory kernel used by GLD into an appropriate
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input matrix for <a class="reference internal" href="#"><span class="doc">fix gle</span></a>. While the GLE scheme is more
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general, the form used by <a class="reference internal" href="fix_gld.html"><span class="doc">fix gld</span></a> can be more directly
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related to the representation of an implicit solvent environment.</p>
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</div>
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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</h2>
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<p>The instantaneous values of the extended variables are written to
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<a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. Because the state of the random
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number generator is not saved in restart files, this means you cannot
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do “exact” restarts with this fix, where the simulation continues on
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the same as if no restart had taken place. However, in a statistical
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sense, a restarted simulation should produce the same behavior.
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Note however that you should use a different seed each time you
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restart, otherwise the same sequence of random numbers will be used
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each time, which might lead to stochastic synchronization and
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subtle artefacts in the sampling.</p>
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<p>This fix can ramp its target temperature over multiple runs, using the
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<em>start</em> and <em>stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command. See the
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<a class="reference internal" href="run.html"><span class="doc">run</span></a> command for details of how to do this.</p>
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<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
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fix to add the energy change induced by Langevin thermostatting to the
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system’s potential energy as part of <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a>.</p>
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<p>This fix computes a global scalar which can be accessed by various
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<a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The scalar is the
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cummulative energy change due to this fix. The scalar value
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calculated by this fix is “extensive”.</p>
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</div>
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<div class="section" id="restrictions">
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<h2>Restrictions</h2>
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<p>The GLE thermostat in its current implementation should not be used
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with rigid bodies, SHAKE or RATTLE. It is expected that all the
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thermostatted degrees of freedom are fully flexible, and the sampled
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ensemble will not be correct otherwise.</p>
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<p>In order to perform constant-pressure simulations please use
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<a class="reference internal" href="fix_press_berendsen.html"><span class="doc">fix press/berendsen</span></a>, rather than
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<a class="reference internal" href="fix_nh.html"><span class="doc">fix npt</span></a>, to avoid duplicate integration of the
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equations of motion.</p>
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<p>This fix is part of the USER-MISC package. It is only enabled if LAMMPS
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was built with that package. See the <a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">Making LAMMPS</span></a> section for more info.</p>
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</div>
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<div class="section" id="related-commands">
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<h2>Related commands</h2>
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<p><a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>, <a class="reference internal" href="fix_viscous.html"><span class="doc">fix viscous</span></a>, <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a>, <a class="reference internal" href="pair_dpd.html"><span class="doc">pair_style dpd/tstat</span></a>, <a class="reference internal" href="fix_gld.html"><span class="doc">fix gld</span></a></p>
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<hr class="docutils" />
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<p id="ceriotti"><strong>(Ceriotti)</strong> Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6,
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1170-80 (2010)</p>
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<p id="gle4md"><strong>(GLE4MD)</strong> <a class="reference external" href="http://epfl-cosmo.github.io/gle4md/">http://epfl-cosmo.github.io/gle4md/</a></p>
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<p id="ceriotti2"><strong>(Ceriotti2)</strong> Ceriotti, Bussi and Parrinello, Phys Rev Lett 103,
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030603 (2009)</p>
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