fix press/berendsen command¶
Syntax¶
fix ID group-ID press/berendsen keyword value ...
ID, group-ID are documented in fix command
press/berendsen = style name of this fix command
one or more keyword value pairs may be appended keyword = iso or aniso or x or y or z or couple or dilate or modulus iso or aniso values = Pstart Pstop Pdamp Pstart,Pstop = scalar external pressure at start/end of run (pressure units) Pdamp = pressure damping parameter (time units) x or y or z values = Pstart Pstop Pdamp Pstart,Pstop = external stress tensor component at start/end of run (pressure units) Pdamp = stress damping parameter (time units) couple = none or xyz or xy or yz or xz modulus value = bulk modulus of system (pressure units) dilate value = all or partial
Examples¶
fix 1 all press/berendsen iso 0.0 0.0 1000.0
fix 2 all press/berendsen aniso 0.0 0.0 1000.0 dilate partial
Description¶
Reset the pressure of the system by using a Berendsen barostat (Berendsen), which rescales the system volume and (optionally) the atoms coordinates within the simulation box every timestep.
Regardless of what atoms are in the fix group, a global pressure is computed for all atoms. Similarly, when the size of the simulation box is changed, all atoms are re-scaled to new positions, unless the keyword dilate is specified with a value of partial, in which case only the atoms in the fix group are re-scaled. The latter can be useful for leaving the coordinates of atoms in a solid substrate unchanged and controlling the pressure of a surrounding fluid.
Note
Unlike the fix npt or fix nph commands which perform Nose/Hoover barostatting AND time integration, this fix does NOT perform time integration. It only modifies the box size and atom coordinates to effect barostatting. Thus you must use a separate time integration fix, like fix nve or fix nvt to actually update the positions and velocities of atoms. This fix can be used in conjunction with thermostatting fixes to control the temperature, such as fix nvt or fix langevin or fix temp/berendsen.
See the Howto baroostat page for a discussion of different ways to perform barostatting.
The barostat is specified using one or more of the iso, aniso, x, y, z, and couple keywords. These keywords give you the ability to specify the 3 diagonal components of an external stress tensor, and to couple various of these components together so that the dimensions they represent are varied together during a constant-pressure simulation. Unlike the fix npt and fix nph commands, this fix cannot be used with triclinic (non-orthogonal) simulation boxes to control all 6 components of the general pressure tensor.
The target pressures for each of the 3 diagonal components of the stress tensor can be specified independently via the x, y, z, keywords, which correspond to the 3 simulation box dimensions. For each component, the external pressure or tensor component at each timestep is a ramped value during the run from Pstart to Pstop. If a target pressure is specified for a component, then the corresponding box dimension will change during a simulation. For example, if the y keyword is used, the y-box length will change. A box dimension will not change if that component is not specified, although you have the option to change that dimension via the fix deform command.
For all barostat keywords, the Pdamp parameter determines the time scale on which pressure is relaxed. For example, a value of 10.0 means to relax the pressure in a timespan of (roughly) 10 time units (tau or fs or ps - see the units command).
Note
A Berendsen barostat will not work well for arbitrary values of Pdamp. If Pdamp is too small, the pressure and volume can fluctuate wildly; if it is too large, the pressure will take a very long time to equilibrate. A good choice for many models is a Pdamp of around 1000 timesteps. However, note that Pdamp is specified in time units, and that timesteps are NOT the same as time units for most units settings.
Note
The relaxation time is actually also a function of the bulk modulus of the system (inverse of isothermal compressibility). The bulk modulus has units of pressure and is the amount of pressure that would need to be applied (isotropically) to reduce the volume of the system by a factor of 2 (assuming the bulk modulus was a constant, independent of density, which it’s not). The bulk modulus can be set via the keyword modulus. The Pdamp parameter is effectively multiplied by the bulk modulus, so if the pressure is relaxing faster than expected or desired, increasing the bulk modulus has the same effect as increasing Pdamp. The converse is also true. LAMMPS does not attempt to guess a correct value of the bulk modulus; it just uses 10.0 as a default value which gives reasonable relaxation for a Lennard-Jones liquid, but will be way off for other materials and way too small for solids. Thus you should experiment to find appropriate values of Pdamp and/or the modulus when using this fix.
The couple keyword allows two or three of the diagonal components of the pressure tensor to be “coupled” together. The value specified with the keyword determines which are coupled. For example, xz means the Pxx and Pzz components of the stress tensor are coupled. Xyz means all 3 diagonal components are coupled. Coupling means two things: the instantaneous stress will be computed as an average of the corresponding diagonal components, and the coupled box dimensions will be changed together in lockstep, meaning coupled dimensions will be dilated or contracted by the same percentage every timestep. The Pstart, Pstop, Pdamp parameters for any coupled dimensions must be identical. Couple xyz can be used for a 2d simulation; the z dimension is simply ignored.
The iso and aniso keywords are simply shortcuts that are equivalent to specifying several other keywords together.
The keyword iso means couple all 3 diagonal components together when pressure is computed (hydrostatic pressure), and dilate/contract the dimensions together. Using “iso Pstart Pstop Pdamp” is the same as specifying these 4 keywords:
x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple xyz
The keyword aniso means x, y, and z dimensions are controlled independently using the Pxx, Pyy, and Pzz components of the stress tensor as the driving forces, and the specified scalar external pressure. Using “aniso Pstart Pstop Pdamp” is the same as specifying these 4 keywords:
x Pstart Pstop Pdamp
y Pstart Pstop Pdamp
z Pstart Pstop Pdamp
couple none
This fix computes a temperature and pressure each timestep. To do this, the fix creates its own computes of style “temp” and “pressure”, as if these commands had been issued:
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp
See the compute temp and compute pressure commands for details. Note that the IDs of the new computes are the fix-ID + underscore + “temp” or fix_ID + underscore + “press”, and the group for the new computes is the same as the fix group.
Note that these are NOT the computes used by thermodynamic output (see the thermo_style command) with ID = thermo_temp and thermo_press. This means you can change the attributes of this fix’s temperature or pressure via the compute_modify command or print this temperature or pressure during thermodynamic output via the thermo_style custom command using the appropriate compute-ID. It also means that changing attributes of thermo_temp or thermo_press will have no effect on this fix.
Restart, fix_modify, output, run start/stop, minimize info¶
No information about this fix is written to binary restart files.
The fix_modify temp and press options are supported by this fix. You can use them to assign a compute you have defined to this fix which will be used in its temperature and pressure calculations. If you do this, note that the kinetic energy derived from the compute temperature should be consistent with the virial term computed using all atoms for the pressure. LAMMPS will warn you if you choose to compute temperature on a subset of atoms.
No global or per-atom quantities are stored by this fix for access by various output commands.
This fix can ramp its target pressure 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¶
Any dimension being adjusted by this fix must be periodic.