Homec4science
Diffusion lammps (lammm-master-deprecated) Browse

lammps/doc/fix_temp_csvr.html
71ebbc359f8clammm-master-deprecated

Last Change
Raw File

fix_temp_csvr.html
View Options

<HTML>
<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>
</CENTER>
<HR>
<H3>fix temp/csvr command
</H3>
<H3>fix temp/csld command
</H3>
<P><B>Syntax:</B>
</P>
<PRE>fix ID group-ID temp/csvr Tstart Tstop Tdamp seed
</PRE>
<PRE>fix ID group-ID temp/csld Tstart Tstop Tdamp seed
</PRE>
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
<LI>temp/csvr or temp/csld = style name of this fix command
<LI>Tstart,Tstop = desired temperature at start/end of run
<PRE> Tstart can be a variable (see below)
</PRE>
<LI>Tdamp = temperature damping parameter (time units)
<LI>seed = random number seed to use for white noise (positive integer)
</UL>
<P><B>Examples:</B>
</P>
<PRE>fix 1 all temp/csvr 300.0 300.0 100.0 54324
</PRE>
<PRE>fix 1 all temp/csld 100.0 300.0 10.0 123321
</PRE>
<P><B>Description:</B>
</P>
<P>Adjust the temperature with a canonical sampling thermostat that uses
global velocity rescaling with Hamiltonian dynamics (<I>temp/csvr</I>)
<A HREF = "#Bussi1">(Bussi1)</A>, or Langevin dynamics (<I>temp/csld</I>)
<A HREF = "#Bussi2">(Bussi2)</A>. In the case of <I>temp/csvr</I> the thermostat is
similar to the empirical Berendsen thermostat in
<A HREF = "fix_temp_berendsen.html">temp/berendsen</A>, but chooses the actual
scaling factor from a suitably chosen (gaussian) distribution rather
than having it determined from the time constant directly. In the case
of <I>temp/csld</I> the velocities are updated to a linear combination of
the current velocities with a gaussian distribution of velocities at
the desired temperature. Both termostats are applied every timestep.
</P>
<P>The thermostat is applied to only the translational degrees of freedom
for the particles, which is an important consideration for finite-size
particles which have rotational degrees of freedom are being
thermostatted with these fixes. The translational degrees of freedom
can also have a bias velocity removed from them before thermostatting
takes place; see the description below.
</P>
<P>The desired temperature at each timestep is a ramped value during the
run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
time units and determines how rapidly the temperature is relaxed. For
example, a value of 100.0 means to relax the temperature in a timespan
of (roughly) 100 time units (tau or fmsec or psec - see the
<A HREF = "units.html">units</A> command).
</P>
<P><I>Tstart</I> can be specified as an equal-style <A HREF = "variable.html">variable</A>.
In this case, the <I>Tstop</I> setting is ignored. If the value is a
variable, it should be specified as v_name, where name is the variable
name. In this case, the variable will be evaluated each timestep, and
its value used to determine the target temperature.
</P>
<P>Equal-style variables can specify formulas with various mathematical
functions, and include <A HREF = "thermo_style.html">thermo_style</A> command
keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent temperature.
</P>
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nh.html">fix nvt</A> command which
performs Nose/Hoover thermostatting AND time integration, these fixes
do NOT perform time integration. They only modify velocities to effect
thermostatting. Thus you must use a separate time integration fix,
like <A HREF = "fix_nve.html">fix nve</A> to actually update the positions of atoms
using the modified velocities. Likewise, these fixes should not
normally be used on atoms that also have their temperature controlled
by another fix - e.g. by <A HREF = "fix_nh.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
langevin</A> commands.
</P>
<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
a discussion of different ways to compute temperature and perform
thermostatting.
</P>
<P>These fixes compute a temperature each timestep. To do this, the fix
creates its own compute of style "temp", as if this command had been
issued:
</P>
<PRE>compute fix-ID_temp group-ID temp
</PRE>
<P>See the <A HREF = "compute_temp.html">compute temp</A> command for details. Note
that the ID of the new compute is the fix-ID + underscore + "temp",
and the group for the new compute is the same as the fix group.
</P>
<P>Note that this is NOT the compute used by thermodynamic output (see
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
custom</A> command using the appropriate compute-ID.
It also means that changing attributes of <I>thermo_temp</I> will have no
effect on this fix.
</P>
<P>Like other fixes that perform thermostatting, these fixes can be used
with <A HREF = "compute.html">compute commands</A> that calculate a temperature
after removing a "bias" from the atom velocities. E.g. removing the
center-of-mass velocity from a group of atoms or only calculating
temperature on the x-component of velocity or only calculating
temperature for atoms in a geometric region. This is not done by
default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
to assign a temperature compute to this fix that includes such a bias
term. See the doc pages for individual <A HREF = "compute.html">compute
commands</A> to determine which ones include a bias. In
this case, the thermostat works in the following manner: the current
temperature is calculated taking the bias into account, bias is
removed from each atom, thermostatting is performed on the remaining
thermal degrees of freedom, and the bias is added back in.
</P>
<HR>
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
</P>
<P>No information about these fixes are written to <A HREF = "restart.html">binary restart
files</A>.
</P>
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by these
fixes. You can use it to assign a temperature <A HREF = "compute.html">compute</A>
you have defined to these fixes which will be used in its thermostatting
procedure, as described above. For consistency, the group used by
these fixes and by the compute should be the same.
</P>
<P>These fixes can ramp its target temperature over multiple runs, using
the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
<A HREF = "run.html">run</A> command for details of how to do this.
</P>
<P>These fixes are not invoked during <A HREF = "minimize.html">energy minimization</A>.
</P>
<P>These fixes compute a global scalar which can be accessed by various
<A HREF = "Section_howto.html#howto_15">output commands</A>. The scalar is the
cummulative energy change due to the fix. The scalar value
calculated by this fix is "extensive".
</P>
<P><B>Restrictions:</B>
</P>
<P>These fixes are not compatible with <A HREF = "fix_shake.html">fix shake</A>.
</P>
<P>The fix can be used with dynamic groups as defined by the
<A HREF = "group.html">group</A> command. Likewise it can be used with groups to
which atoms are added or deleted over time, e.g. a deposition
simulation. However, the conservation properties of the thermostat
and barostat are defined for systems with a static set of atoms. You
may observe odd behavior if the atoms in a group vary dramatically
over time or the atom count becomes very small.
</P>
<P><B>Related commands:</B>
</P>
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nh.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
temp/rescale</A>, <A HREF = "fix_langevin.html">fix langevin</A>,
<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp.html">compute temp</A>,
<A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>
</P>
<P><B>Default:</B> none
</P>
<HR>
<A NAME = "Bussi1"></A>
<A NAME = "Bussi2"></A><B>(Bussi1)</B> Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007)
<P><B>(Bussi2)</B> Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007)
</P>
</HTML>
c4science · Help