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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2013-02-16 01:36:33 +08:00
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<H3>fix nvt/sllod/omp command
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</H3>
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2007-06-20 21:15:18 +08:00
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<P><B>Syntax:</B>
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</P>
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2010-04-03 00:51:06 +08:00
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<PRE>fix ID group-ID nvt/sllod keyword value ...
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2007-06-20 21:15:18 +08:00
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</PRE>
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2010-04-03 00:51:06 +08:00
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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>additional thermostat related keyword/value pairs from the <A HREF = "fix_nh.html">fix nvt</A> command can be appended
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2007-06-20 21:15:18 +08:00
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</UL>
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<P><B>Examples:</B>
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</P>
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2010-04-03 00:51:06 +08:00
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<PRE>fix 1 all nvt/sllod temp 300.0 300.0 100.0
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fix 1 all nvt/sllod temp 300.0 300.0 100.0 drag 0.2
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2007-06-20 21:15:18 +08:00
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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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2014-12-20 06:44:45 +08:00
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<P>The SLLOD equations of motion, originally proposed by Hoover and Ladd
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(see <A HREF = "#Evans">(Evans and Morriss)</A>), were proven to be identical to
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Newton's equations of motion for all forms of homogeneous flow by
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<A HREF = "#Daivis">(Daivis and Todd)</A>. As implemented in LAMMPS, they are
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coupled to a Nose/Hoover chain thermostat in a velocity Verlet
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formulation, closely following the implementation used for the <A HREF = "fix_nh.html">fix
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nvt</A> command.
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2007-06-20 21:15:18 +08:00
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</P>
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2010-04-03 00:51:06 +08:00
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<P>Additional parameters affecting the thermostat are specified by
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keywords and values documented with the <A HREF = "fix_nh.html">fix nvt</A>
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command. See, for example, discussion of the <I>temp</I> and <I>drag</I>
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keywords.
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2007-06-20 21:15:18 +08:00
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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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2008-03-01 09:13:20 +08:00
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during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
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2007-06-20 21:15:18 +08:00
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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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2008-03-20 06:51:12 +08:00
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<P>Like other fixes that perform thermostatting, this fix can be used
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with <A HREF = "compute.html">compute commands</A> that calculate a temperature
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after removing a "bias" from the atom velocities. E.g. removing the
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center-of-mass velocity from a group of atoms or only calculating
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temperature on the x-component of velocity or only calculating
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temperature for atoms in a geometric region. This is not done by
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default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
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to assign a temperature compute to this fix that includes such a bias
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term. See the doc pages for individual <A HREF = "compute.html">compute
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commands</A> to determine which ones include a bias. In
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this case, the thermostat works in the following manner: the current
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temperature is calculated taking the bias into account, bias is
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removed from each atom, thermostatting is performed on the remaining
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thermal degrees of freedom, and the bias is added back in.
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</P>
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2013-02-16 01:36:33 +08:00
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<HR>
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2014-08-15 00:30:25 +08:00
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<P>Styles with a <I>cuda</I>, <I>gpu</I>, <I>intel</I>, <I>kk</I>, <I>omp</I>, or <I>opt</I> suffix are
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functionally the same as the corresponding style without the suffix.
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They have been optimized to run faster, depending on your available
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hardware, as discussed in <A HREF = "Section_accelerate.html">Section_accelerate</A>
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of the manual. The accelerated styles take the same arguments and
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should produce the same results, except for round-off and precision
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issues.
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</P>
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<P>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
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KOKKOS, USER-OMP and OPT packages, respectively. They are only
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enabled if LAMMPS was built with those packages. See the <A HREF = "Section_start.html#start_3">Making
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LAMMPS</A> section for more info.
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2013-02-16 01:36:33 +08:00
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</P>
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<P>You can specify the accelerated styles explicitly in your input script
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by including their suffix, or you can use the <A HREF = "Section_start.html#start_7">-suffix command-line
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switch</A> when you invoke LAMMPS, or you can
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use the <A HREF = "suffix.html">suffix</A> command in your input script.
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</P>
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<P>See <A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual for
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more instructions on how to use the accelerated styles effectively.
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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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2010-04-03 00:51:06 +08:00
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<P>This fix computes the same global scalar and global vector of
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quantities as does the <A HREF = "fix_nh.html">fix nvt</A> command.
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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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2010-08-23 23:14:40 +08:00
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<P><B>Restrictions:</B>
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</P>
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2010-09-02 04:48:58 +08:00
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<P>This fix works best without Nose-Hoover chain thermostats, i.e. using
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tchain = 1. Setting tchain to larger values can result in poor
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equilibration.
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2007-06-20 21:15:18 +08:00
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</P>
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<P><B>Related commands:</B>
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</P>
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2010-04-03 00:51:06 +08:00
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<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
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temp/rescale</A>, <A HREF = "fix_langevin.html">fix langevin</A>,
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<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp_deform.html">compute
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temp/deform</A>
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2007-06-20 21:15:18 +08:00
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</P>
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2010-09-02 04:48:58 +08:00
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<P><B>Default:</B>
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</P>
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<P>Same as <A HREF = "fix_nh.html">fix nvt</A>, except tchain = 1.
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2007-06-20 21:15:18 +08:00
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</P>
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<HR>
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2014-12-20 06:44:45 +08:00
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<A NAME = "Evans"></A>
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2007-06-20 21:15:18 +08:00
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2014-12-20 06:44:45 +08:00
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<P><B>(Evans and Morriss)</B> Evans and Morriss, Phys Rev A, 30, 1528 (1984).
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</P>
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<A NAME = "Daivis"></A>
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<P><B>(Daivis and Todd)</B> Daivis and Todd, J Chem Phys, 124, 194103 (2006).
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2007-06-20 21:15:18 +08:00
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</P>
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</HTML>
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