2007-06-20 21:15:18 +08:00
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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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<HR>
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<H3>fix nvt/sllod 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 group-ID nvt/sllod Tstart Tstop Tdamp keyword value ...
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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>nvt/sllod = style name of this fix command
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<LI>Tstart,Tstop = desired temperature at start/end of run
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<LI>Tdamp = temperature damping parameter (time units)
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2007-07-03 04:04:44 +08:00
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<LI>zero or more keyword/value pairs may be appended
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2007-06-20 21:15:18 +08:00
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<LI>keyword = <I>drag</I>
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<PRE> <I>drag</I> value = drag factor added to thermostat (0.0 = no drag)
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all nvt/sllod 300.0 300.0 100.0
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fix 1 all nvt/sllod 300.0 300.0 100.0 drag 0.2
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Perform constant NVT integration to update positions and velocities
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each timestep for atoms in the group using a Nose/Hoover temperature
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thermostat. V is volume; T is temperature. This creates a system
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trajectory consistent with the canonical ensemble.
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</P>
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<P>This thermostat is used for a simulation box that is changing size
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and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
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The size/shape change is induced by use of the <A HREF = "fix_deform.html">fix
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deform</A> command, so each point in the simulation box
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can be thought of as having a "streaming" velocity. This
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position-dependent streaming velocity is subtracted from each atom's
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actual velocity to yield a thermal velocity which is used for
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temperature computation and thermostatting. For example, if the box
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is being sheared in x, relative to y, then points at the bottom of the
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box (low y) have a small x velocity, while points at the top of the
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box (hi y) have a large x velocity. These velocities do not
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contribute to the thermal "temperature" of the atom.
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</P>
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<P>IMPORTANT NOTE: <A HREF = "fix_deform.html">Fix deform</A> has an option for
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remapping either atom coordinates or velocities to the changing
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simulation box. To use fix nvt/sllod, fix deform should NOT remap
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atom positions, because fix nvt/sllod adjusts the atom positions and
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velocities to create a velocity profile that matches the changing box
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2007-06-23 07:41:35 +08:00
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size/shape. Fix deform SHOULD remap atom velocities when atoms cross
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2007-06-20 21:15:18 +08:00
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periodic boundaries since that is consistent with maintaining the
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2007-06-23 07:41:35 +08:00
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velocity profile created by fix nvt/sllod. LAMMPS will give an
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error if this setting is not consistent.
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2007-06-20 21:15:18 +08:00
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</P>
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<P>The SLLOD equations of motion coupled to a Nose/Hoover thermostat are
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discussed in <A HREF = "#Tuckerman">(Tuckerman)</A> (eqs 4 and 5), which is what is
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implemented in LAMMPS in a velocity Verlet formulation.
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</P>
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<P>The desired temperature at each timestep is a ramped value during the
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2007-06-26 08:03:39 +08:00
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run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
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time units and determines how rapidly the temperature is relaxed. For
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example, a value of 100.0 means to relax the temperature in a timespan
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of (roughly) 100 time units (tau or fmsec or psec - see the
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<A HREF = "units.html">units</A> command).
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2007-06-20 21:15:18 +08:00
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</P>
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<P>In some cases (e.g. for solids) the temperature of the system can
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oscillate undesirably when a Nose/Hoover thermostat is applied. The
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optional <I>drag</I> keyword will damp these oscillations, although it
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alters the Nose/Hoover equations. A value of 0.0 (no drag) leaves the
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Nose/Hoover formalism unchanged. A non-zero value adds a drag term;
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the larger the value specified, the greater the damping effect.
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Performing a short run and monitoring the temperature is the best way
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to determine if the drag term is working. Typically a value between
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0.2 to 2.0 is sufficient to damp oscillations after a few periods.
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</P>
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<P>This fix computes a temperature each timestep. To do this, the fix
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creates its own compute of style "temp/deform", as if this command had
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been issued:
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</P>
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<PRE>compute fix-ID_temp group-ID temp/deform
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</PRE>
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2008-01-04 08:37:21 +08:00
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<P>See the <A HREF = "compute_temp_deform.html">compute temp/deform</A> command for
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details. Note that the ID of the new compute is the fix-ID +
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underscore + "temp", and the group for the new compute is the same as
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the fix group.
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2007-06-20 21:15:18 +08:00
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</P>
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<P>Note that this is NOT the compute used by thermodynamic output (see
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the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
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This means you can change the attributes of this fix's temperature
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(e.g. its degrees-of-freedom) via the
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<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
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during thermodyanmic output via the <A HREF = "thermo_style.html">thermo_style
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custom</A> command using the appropriate compute-ID.
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It also means that changing attributes of <I>thermo_temp</I> will have no
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2007-06-26 08:03:39 +08:00
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effect on this fix.
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</P>
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2007-10-11 06:28:11 +08:00
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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2007-06-26 08:03:39 +08:00
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</P>
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<P>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
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restart files</A>. See the <A HREF = "read_restart.html">read_restart</A>
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command for info on how to re-specify a fix in an input script that
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reads a restart file, so that the operation of the fix continues in an
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uninterrupted fashion.
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</P>
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<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
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fix. You can use it to assign a <A HREF = "compute.html">compute</A> you have
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defined to this fix which will be used in its thermostatting
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procedure.
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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 Nose/Hoover thermostatting to
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the 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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2007-10-10 02:24:42 +08:00
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<P>The potential energy change due to this fix is stored as a scalar
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quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
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commands</A>.
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2007-06-26 08:03:39 +08:00
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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>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
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2007-06-20 21:15:18 +08:00
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>The final Tstop cannot be 0.0 since it would make the target T = 0.0
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at some timestep during the simulation which is not allowed in
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the Nose/Hoover formulation.
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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_nve.html">fix nve</A>, <A HREF = "fix_npt.html">fix npt</A>, <A HREF = "fix_npt.html">fix
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npt</A>, <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>, <A HREF = "fix_langevin.html">fix
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langevin</A>, <A HREF = "fix_modify.html">fix_modify</A>,
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2008-01-04 08:37:21 +08:00
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<A HREF = "compute_temp.html">compute temp</A>
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2007-06-20 21:15:18 +08:00
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</P>
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<P><B>Default:</B>
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</P>
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<P>The keyword defaults are drag = 0.0.
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</P>
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<HR>
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<A NAME = "Tuckerman"></A>
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<P><B>(Tuckerman)</B> Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys,
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106, 5615 (1997).
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</P>
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</HTML>
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