forked from lijiext/lammps
213 lines
9.5 KiB
HTML
213 lines
9.5 KiB
HTML
<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 press/berendsen command
|
|
</H3>
|
|
<P><B>Syntax:</B>
|
|
</P>
|
|
<PRE>fix ID group-ID press/berendsen p-style args keyword value ...
|
|
</PRE>
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
|
|
|
<LI>press/berendsen = style name of this fix command
|
|
|
|
<LI>p-style = <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>aniso</I>
|
|
|
|
<PRE> <I>xyz</I> args = Pstart Pstop Pdamp
|
|
Pstart,Pstop = desired pressure at start/end of run (pressure units)
|
|
Pdamp = pressure damping parameter (time units)
|
|
<I>xy</I> or <I>yz</I> or <I>xz</I> args = Px0 Px1 Py0 Py1 Pz0 Pz1 Pdamp
|
|
Px0,Px1,Py0,Py1,Pz0,Pz1 = desired pressure in x,y,z at
|
|
start/end (0/1) of run (pressure units)
|
|
Pdamp = pressure damping parameter (time units)
|
|
<I>aniso</I> args = Px0 Px1 Py0 Py1 Pz0 Pz1 Pdamp
|
|
Px0,Px1,Py0,Py1,Pz0,Pz1 = desired pressure in x,y,z at
|
|
start/end (0/1) of run (pressure units)
|
|
Pdamp = pressure damping parameter (time units)
|
|
</PRE>
|
|
<LI>zero or more keyword/value pairs may be appended
|
|
|
|
<LI>keyword = <I>dilate</I> or <I>modulus</I>
|
|
|
|
<PRE> <I>dilate</I> value = <I>all</I> or <I>partial</I>
|
|
<I>modulus</I> value = bulk modulus of system (pressure units)
|
|
</PRE>
|
|
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>fix 1 all press/berendsen xyz 0.0 0.0 1000.0
|
|
fix 2 all press/berendsen aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial
|
|
</PRE>
|
|
<P><B>Description:</B>
|
|
</P>
|
|
<P>Reset the pressure of the system by using a Berendsen barostat
|
|
<A HREF = "#Berendsen">(Berendsen)</A>, which rescales the system volume and
|
|
(optionally) the atoms coordinates withing the simulation box every
|
|
timestep.
|
|
</P>
|
|
<P>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 <I>dilate</I> is specified with a value of <I>partial</I>, 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.
|
|
</P>
|
|
<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_npt.html">fix npt</A> or <A HREF = "fix_nph.html">fix
|
|
nph</A> 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 <A HREF = "fix_nve.html">fix
|
|
nve</A> or <A HREF = "fix_nvt.html">fix nvt</A> 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 <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix langevin</A> or <A HREF = "fix_temp_berendsen,html">fix
|
|
temp/berendsen</A>.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The pressure can be controlled in one of several styles, as specified
|
|
by the <I>p-style</I> argument. In each case, the desired pressure at each
|
|
timestep is a ramped value during the run from the starting value to
|
|
the end value.
|
|
</P>
|
|
<P>Style <I>xyz</I> means couple all dimensions together when pressure is
|
|
computed (isotropic pressure), and dilate/contract the dimensions
|
|
together.
|
|
</P>
|
|
<P>Styles <I>xy</I> or <I>yz</I> or <I>xz</I> means that the 2 specified dimensions are
|
|
coupled together, both for pressure computation and for
|
|
dilation/contraction. The 3rd dimension dilates/contracts
|
|
independently, using its pressure component as the driving force.
|
|
These styles cannot be used for a 2d simulation.
|
|
</P>
|
|
<P>For style <I>aniso</I>, all dimensions dilate/contract independently using
|
|
their individual pressure components as the driving forces.
|
|
</P>
|
|
<P>For any of the styles except <I>xyz</I>, any of the independent pressure
|
|
components (e.g. z in <I>xy</I>, or any dimension in <I>aniso</I>) can have
|
|
their target pressures (both start and stop values) specified as NULL.
|
|
This means that no pressure control is applied to that dimension so
|
|
that the box dimension remains unchanged. For a 2d simulation the z
|
|
pressure components must be specified as NULL when using style
|
|
<I>aniso</I>.
|
|
</P>
|
|
<P>In some cases (e.g. for solids) the pressure (volume) and/or
|
|
temperature of the system can oscillate undesirably when a Nose/Hoover
|
|
barostat is applied. The optional <I>drag</I> 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
|
|
pressure 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.
|
|
</P>
|
|
<P>For all pressure styles, the simulation box stays rectangular in
|
|
shape. Parinello-Rahman boundary conditions (tilted box) for this fix
|
|
are not yet implemented in LAMMPS.
|
|
</P>
|
|
<P>For all styles, the <I>Pdamp</I> parameter determines the time scale on
|
|
which pressure is relaxed. For example, a value of 1000.0 means to
|
|
relax the pressure in a timespan of (roughly) 1000 time units (tau or
|
|
fmsec or psec - see the <A HREF = "units.html">units</A> command).
|
|
</P>
|
|
<P>IMPORTANT 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 <I>modulus</I>. The <I>Pdamp</I> 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 <I>Pdamp</I>. 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 <I>Pdamp</I> and/or the <I>modulus</I> when using this fix.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>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:
|
|
</P>
|
|
<PRE>compute fix-ID_temp group-ID temp
|
|
compute fix-ID_press group-ID pressure fix-ID_temp
|
|
</PRE>
|
|
<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html">compute
|
|
pressure</A> 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.
|
|
</P>
|
|
<P>Note that these are NOT the computes used by thermodynamic output (see
|
|
the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
|
|
and <I>thermo_press</I>. This means you can change the attributes of this
|
|
fix's temperature or pressure via the
|
|
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
|
|
or pressure 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> or
|
|
<I>thermo_press</I> will have no effect on this fix.
|
|
</P>
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
|
</P>
|
|
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
|
files</A>.
|
|
</P>
|
|
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
|
|
supported by this fix. You can use them to assign a
|
|
<A HREF = "compute.html">compute</A> 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.
|
|
</P>
|
|
<P>No global scalar or vector or per-atom quantities are stored by this
|
|
fix for access by various <A HREF = "Section_howto.html#4_15">output commands</A>.
|
|
</P>
|
|
<P>This fix can ramp its target pressure 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>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
|
|
</P>
|
|
<P><B>Restrictions:</B>
|
|
</P>
|
|
<P>Any dimension being adjusted by this fix must be periodic. A
|
|
dimension whose target pressures are specified as NULL can be
|
|
non-periodic or periodic.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nph.html">fix nph</A>, <A HREF = "fix_npt.html">fix
|
|
npt</A>, <A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>,
|
|
<A HREF = "fix_modify.html">fix_modify</A>
|
|
</P>
|
|
<P><B>Default:</B>
|
|
</P>
|
|
<P>The keyword defaults are dilate = all, modulus = 10.0 in units of
|
|
pressure for whatever <A HREF = "units.html">units</A> are defined.
|
|
</P>
|
|
<HR>
|
|
|
|
<A NAME = "Berendsen"></A>
|
|
|
|
<P><B>(Berendsen)</B> Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
|
|
Phys, 81, 3684 (1984).
|
|
</P>
|
|
</HTML>
|