lammps/doc/fix_nvt_sllod.txt

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)

:line

fix nvt/sllod command :h3

[Syntax:]

fix ID group-ID nvt/sllod Tstart Tstop Tdamp keyword value ... :pre

ID, group-ID are documented in "fix"_fix.html command :ulb,l
nvt/sllod = style name of this fix command :l
Tstart,Tstop = desired temperature at start/end of run :l
Tdamp = temperature damping parameter (time units) :l

zero or more keyword/value pairs may be appended :l
keyword = {drag} :l
  {drag} value = drag factor added to thermostat (0.0 = no drag) :pre
:ule

[Examples:]

fix 1 all nvt/sllod 300.0 300.0 100.0
fix 1 all nvt/sllod 300.0 300.0 100.0 drag 0.2 :pre

[Description:]

Perform constant NVT integration to update positions and velocities
each timestep for atoms in the group using a Nose/Hoover temperature
thermostat.  V is volume; T is temperature.  This creates a system
trajectory consistent with the canonical ensemble. 

This thermostat is used for a simulation box that is changing size
and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
The size/shape change is induced by use of the "fix
deform"_fix_deform.html command, so each point in the simulation box
can be thought of as having a "streaming" velocity.  This
position-dependent streaming velocity is subtracted from each atom's
actual velocity to yield a thermal velocity which is used for
temperature computation and thermostatting.  For example, if the box
is being sheared in x, relative to y, then points at the bottom of the
box (low y) have a small x velocity, while points at the top of the
box (hi y) have a large x velocity.  These velocities do not
contribute to the thermal "temperature" of the atom.

IMPORTANT NOTE: "Fix deform"_fix_deform.html has an option for
remapping either atom coordinates or velocities to the changing
simulation box.  To use fix nvt/sllod, fix deform should NOT remap
atom positions, because fix nvt/sllod adjusts the atom positions and
velocities to create a velocity profile that matches the changing box
size/shape.  Fix deform SHOULD remap atom velocities when atoms cross
periodic boundaries since that is consistent with maintaining the
velocity profile created by fix nvt/sllod.  LAMMPS will give an
error if this setting is not consistent.

The SLLOD equations of motion coupled to a Nose/Hoover thermostat are
discussed in "(Tuckerman)"_#Tuckerman (eqs 4 and 5), which is what is
implemented in LAMMPS in a velocity Verlet formulation.

The desired temperature at each timestep is a ramped value during the
run from {Tstart} to {Tstop}.  The {Tdamp} 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
"units"_units.html command).

In some cases (e.g. for solids) the temperature of the system can
oscillate undesirably when a Nose/Hoover thermostat is applied.  The
optional {drag} keyword will damp these oscillations, although it
alters the Nose/Hoover equations.  A value of 0.0 (no drag) leaves the
Nose/Hoover formalism unchanged.  A non-zero value adds a drag term;
the larger the value specified, the greater the damping effect.
Performing a short run and monitoring the temperature is the best way
to determine if the drag term is working.  Typically a value between
0.2 to 2.0 is sufficient to damp oscillations after a few periods.

This fix computes a temperature each timestep.  To do this, the fix
creates its own compute of style "temp/deform", as if this command had
been issued:

compute fix-ID_temp group-ID temp/deform :pre

See the "compute temp/deform"_compute_temp_deform.html 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.

Note that this is NOT the compute used by thermodynamic output (see
the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
This means you can change the attributes of this fix's temperature
(e.g. its degrees-of-freedom) via the
"compute_modify"_compute_modify.html command or print this temperature
during thermodynamic output via the "thermo_style
custom"_thermo_style.html command using the appropriate compute-ID.
It also means that changing attributes of {thermo_temp} will have no
effect on this fix.

Like other fixes that perform thermostatting, this fix can be used
with "compute commands"_compute.html 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 "fix_modify"_fix_modify.html command is used
to assign a temperature compute to this fix that includes such a bias
term.  See the doc pages for individual "compute
commands"_compute.html 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.

[Restart, fix_modify, output, run start/stop, minimize info:]

This fix writes the state of the Nose/Hoover thermostat to "binary
restart files"_restart.html.  See the "read_restart"_read_restart.html
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.

The "fix_modify"_fix_modify.html {temp} option is supported by this
fix.  You can use it to assign a "compute"_compute.html you have
defined to this fix which will be used in its thermostatting
procedure.

The "fix_modify"_fix_modify.html {energy} option is supported by this
fix to add the energy change induced by Nose/Hoover thermostatting to
the system's potential energy as part of "thermodynamic
output"_thermo_style.html.

The cummulative energy change due to this fix is stored as a scalar
quantity, which can be accessed by various "output
commands"_Section_howto.html#4_15.  The scalar value calculated by
this fix is "extensive".

This fix can ramp its target temperature over multiple runs, using the
{start} and {stop} keywords of the "run"_run.html command.  See the
"run"_run.html command for details of how to do this.

This fix is not invoked during "energy minimization"_minimize.html.

[Restrictions:]

The final Tstop cannot be 0.0 since it would make the target T = 0.0
at some timestep during the simulation which is not allowed in 
the Nose/Hoover formulation.

[Related commands:]

"fix nve"_fix_nve.html, "fix npt"_fix_npt.html, "fix
npt"_fix_npt.html, "fix temp/rescale"_fix_temp_rescale.html, "fix
langevin"_fix_langevin.html, "fix_modify"_fix_modify.html,
"compute temp"_compute_temp.html

[Default:]

The keyword defaults are drag = 0.0.

:line

:link(Tuckerman)
[(Tuckerman)] Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys,
106, 5615 (1997).