forked from lijiext/lammps
171 lines
7.3 KiB
HTML
171 lines
7.3 KiB
HTML
<HTML>
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<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
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<H3>fix gle command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID id-group gle Ns Tstart Tstop seed Amatrix [noneq Cmatrix] [every stride]
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>gle = style name of this fix command
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<LI>Ns = number of additional fictitious momenta
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<LI>Tstart, Tstop = temperature ramp during the run
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<LI>Amatrix = file to read the drift matrix A from
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<LI>seed = random number seed to use for generating noise (positive integer)
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<LI>zero or more keyword/value pairs may be appended
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keyword = <I>noneq</I> and/or <I>every</I>
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<I>noneq</I> Cmatrix = file to read the non-equilibrium covariance matrix from
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<I>every</I> stride = apply the GLE once every time steps. Reduces the accuracy
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of the integration of the GLE, but has *no effect* on the accuracy of equilibrium
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sampling. It might change sampling properties when used together with <I>noneq</I>.
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</UL>
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<P><B>Examples:</B>
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</P>
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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
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</P>
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<P><B>Description:</B>
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</P>
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<P>Apply a Generalized Langevin Equation (GLE) thermostat as described
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in <A HREF = "#Ceriotti">(Ceriotti)</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 HREF = "fix_langevin.html">fix langevin</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 HREF = "fix_nve.html">fix nve</A> -- at least not
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on the same atom groups.
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</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
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</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
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</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.
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</P>
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<P>The drift matrix should be given as an external file <I>Afile</I>,
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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 HREF = "#GLE4MD">(GLE4MD)</A>.
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</P>
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<P>Equilibrium sampling a temperature T is obtained by specifiying the
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target value as the <I>Tstart</I> and <I>Tstop</I> 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 HREF = "#Ceriotti2">(Ceriotti2)</A>. This is achieved specifying the
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<I>noneq</I> keyword followed by the name of the file that contains the
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static covariance matrix for the non-equilibrium dynamics.
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</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 <I>every</I> 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.
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</P>
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<P>The random number <I>seed</I> 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.
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</P>
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<P>Note also that the Generalized Langevin Dynamics scheme that is
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implemented by the <A HREF = "fix_gld.html">fix gld</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 HREF = "fix_gle.html">fix_gle</A>. While the GLE scheme is more
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general, the form used by <A HREF = "fix_gld.html">fix gld</A> can be more directly
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related to the representation of an implicit solvent environment.
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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>The instantaneous values of the extended variables are written to
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<A HREF = "restart.html">binary restart files</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.
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</P>
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<P>This fix can ramp its target temperature over multiple runs, using the
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<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
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<A HREF = "run.html">run</A> command for details of how to do this.
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</P>
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<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> 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 HREF = "thermo_style.html">thermodynamic
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output</A>.
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</P>
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<P>This fix computes a global scalar which can be accessed by various
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<A HREF = "Section_howto.html#howto_15">output commands</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".
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</P>
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<P><B>Restrictions:</B>
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</P>
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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.
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</P>
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<P>In order to perform constant-pressure simulations please use
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<A HREF = "fix_press_berendsen.html">fix press/berendsen</A>, rather than
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<A HREF = "fix_npt.html">fix_npt</A>, to avoid duplicate integration of the
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equations of motion.
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</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 HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_viscous.html">fix
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viscous</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "pair_dpd.html">pair_style
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dpd/tstat</A>, <A HREF = "fix_gld.html">fix_gld</A>
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</P>
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<HR>
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<A NAME = "Ceriotti"></A>
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<P><B>(Ceriotti)</B> Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6,
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1170-80 (2010)
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</P>
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<A NAME = "GLE4MD"></A>
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<P><B>(GLE4MD)</B> <A HREF = "http://epfl-cosmo.github.io/gle4md/">http://epfl-cosmo.github.io/gle4md/</A>
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</P>
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<A NAME = "Ceriotti2"></A>
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<P><B>(Ceriotti2)</B> Ceriotti, Bussi and Parrinello, Phys Rev Lett 103,
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030603 (2009)
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</P>
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</HTML>
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