2008-03-12 01:15:19 +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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<H3>fix temp/berendsen command
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</H3>
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2011-06-09 05:46:03 +08:00
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<H3>fix temp/berendsen/cuda command
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</H3>
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2008-03-12 01:15:19 +08:00
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID temp/berendsen Tstart Tstop Tdamp
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</PRE>
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2012-05-24 21:31:42 +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>temp/berendsen = style name of this fix command
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<LI>Tstart,Tstop = desired temperature at start/end of run
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<PRE> Tstart can be a variable (see below)
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</PRE>
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2008-03-12 01:15:19 +08:00
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<LI>Tdamp = temperature damping parameter (time units)
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</UL>
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<P><B>Examples:</B>
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</P>
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2009-04-11 04:27:15 +08:00
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<PRE>fix 1 all temp/berendsen 300.0 300.0 100.0
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2008-03-12 01:15:19 +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>Reset the temperature of a group of atoms by using a Berendsen
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2008-03-18 04:49:34 +08:00
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thermostat <A HREF = "#Berendsen">(Berendsen)</A>, which rescales their velocities
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2008-03-12 01:15:19 +08:00
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every timestep.
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</P>
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2008-03-20 06:51:12 +08:00
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<P>The thermostat is applied to only the translational degrees of freedom
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for the particles, which is an important consideration if extended
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spherical or aspherical particles which have rotational degrees of
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freedom are being thermostatted with this fix. The translational
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degrees of freedom can also have a bias velocity removed from them
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before thermostatting takes place; see the description below.
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</P>
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2008-03-12 01:15:19 +08:00
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<P>The desired temperature at each timestep is a ramped value during the
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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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</P>
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2012-05-24 21:31:42 +08:00
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<P><I>Tstart</I> can be specified as an equal-style <A HREF = "variable.html">variable</A>.
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In this case, the <I>Tstop</I> setting is ignored. If the value is a
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variable, it should be specified as v_name, where name is the variable
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name. In this case, the variable will be evaluated each timestep, and
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its value used to determine the target temperature.
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</P>
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<P>Equal-style variables can specify formulas with various mathematical
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functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
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keywords for the simulation box parameters and timestep and elapsed
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time. Thus it is easy to specify a time-dependent temperature.
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</P>
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2010-04-03 00:51:06 +08:00
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<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</A> command which
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2008-03-12 01:15:19 +08:00
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performs Nose/Hoover thermostatting AND time integration, this fix
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does NOT perform time integration. It only modifies velocities to
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effect thermostatting. Thus you must use a separate time integration
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fix, like <A HREF = "fix_nve.html">fix nve</A> to actually update the positions of
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atoms using the modified velocities. Likewise, this fix should not
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normally be used on atoms that also have their temperature controlled
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2010-04-03 00:51:06 +08:00
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by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
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2008-03-12 01:15:19 +08:00
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langevin</A> commands.
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</P>
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2011-08-26 01:01:01 +08:00
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<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
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a discussion of different ways to compute temperature and perform
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2008-04-05 05:15:50 +08:00
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thermostatting.
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</P>
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2008-03-12 01:15:19 +08:00
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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", as if this command had been
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issued:
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</P>
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<PRE>compute fix-ID_temp group-ID temp
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</PRE>
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<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details. Note
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that the ID of the new compute is the fix-ID + underscore + "temp",
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and the group for the new compute is the same as the fix group.
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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 thermodynamic 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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effect on this fix.
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</P>
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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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2011-06-09 05:46:03 +08:00
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<HR>
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<P>Styles with a <I>cuda</I> suffix are functionally the same as the
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corresponding style without the suffix. They have been optimized to
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run faster, depending on your available hardware, as discussed in
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2011-12-14 04:35:35 +08:00
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<A HREF = "Section_accelerate.html">Section_accelerate</A> of the manual. The
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accelerated styles take the same arguments and should produce the same
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results, except for round-off and precision issues.
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2011-06-09 05:46:03 +08:00
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</P>
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2011-08-27 02:53:00 +08:00
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<P>These accelerated styles are part of the USER-CUDA package. They are
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only enabled if LAMMPS 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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2011-06-09 05:46:03 +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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2012-01-28 07:39:14 +08:00
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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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2011-08-26 00:46:23 +08:00
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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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2011-06-09 05:46:03 +08:00
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</P>
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2011-12-14 04:35:35 +08:00
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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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2011-06-09 05:46:03 +08:00
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</P>
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<HR>
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2008-03-12 01:15:19 +08:00
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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>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>.
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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 temperature <A HREF = "compute.html">compute</A>
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you have defined to this fix which will be used in its thermostatting
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procedure, as described above. For consistency, the group used by
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this fix and by the compute should be the same.
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</P>
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2010-09-11 01:31:34 +08:00
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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 implied by a velocity rescaling 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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2011-08-26 01:01:01 +08:00
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<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
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2010-09-11 01:31:34 +08:00
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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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2008-03-12 01:15:19 +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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</P>
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<P><B>Restrictions:</B> none
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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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2008-03-12 01:15:19 +08:00
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temp/rescale</A>, <A HREF = "fix_langevin.html">fix langevin</A>,
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2008-03-18 04:49:34 +08:00
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<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp.html">compute temp</A>,
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<A HREF = "fix_press_berendsen.html">fix press/berendsen</A>
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2008-03-12 01:15:19 +08:00
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</P>
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<P><B>Default:</B> none
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</P>
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<HR>
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<A NAME = "Berendsen"></A>
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<P><B>(Berendsen)</B> Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
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Phys, 81, 3684 (1984).
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</P>
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</HTML>
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