Syntax:
fix ID group-ID nvt/sllod Tstart Tstop Tdamp keyword value ...
drag value = drag factor added to thermostat (0.0 = no drag)
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
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 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 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) (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 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
See the compute temp/deform command for details. Note that the ID of the new compute is the fix-ID with underscore + "temp" appended 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 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 command or print this temperature during thermodyanmic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp will have no effect on this fix.
Restart, fix_modify, output, run start/stop, minimize info:
This fix writes the state of the Nose/Hoover thermostat to binary restart files. See the read_restart 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 temp option is supported by this fix. You can use it to assign a compute you have defined to this fix which will be used in its thermostatting procedure.
The fix_modify 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.
The potential energy change due to this fix is stored as a scalar quantity, which can be accessed by various output commands.
This fix can ramp its target temperature over multiple runs, using the start and stop keywords of the run command. See the run command for details of how to do this.
This fix is not invoked during energy minimization.
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 npt, fix npt, fix temp/rescale, fix langevin, fix_modify, temperature
Default:
The keyword defaults are drag = 0.0.
(Tuckerman) Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, 106, 5615 (1997).