2006-09-22 00:22:34 +08:00
|
|
|
<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 npt command
|
|
|
|
|
</H3>
|
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>fix ID group-ID npt Tstart Tstop Tdamp p-style args keyword value ...
|
|
|
|
|
</PRE>
|
|
|
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
|
|
|
|
|
|
|
|
|
<LI>npt = style name of this fix command
|
|
|
|
|
|
|
|
|
|
<LI>Tstart,Tstop = desired temperature at start/end of run
|
|
|
|
|
|
|
|
|
|
<LI>Tdamp = temperature damping parameter (time units)
|
|
|
|
|
|
|
|
|
|
<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> or <I>aniso</I> args = Px_start Px_stop Py_start Py_stop Pz_start Pz_stop Pdamp
|
|
|
|
|
Px_start,Px_stop,... = desired pressure in x,y,z at start/end of run (pressure units)
|
|
|
|
|
Pdamp = pressure damping parameter (time units)
|
|
|
|
|
</PRE>
|
2007-07-03 04:04:44 +08:00
|
|
|
<LI>zero or more keyword/value pairs may be appended
|
2006-09-22 00:22:34 +08:00
|
|
|
|
|
|
|
|
<LI>keyword = <I>drag</I> or <I>dilate</I>
|
|
|
|
|
|
|
|
|
|
<PRE> <I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
|
|
|
|
|
<I>dilate</I> value = <I>all</I> or <I>partial</I>
|
|
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
|
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<PRE>fix 1 all npt 300.0 300.0 100.0 xyz 0.0 0.0 1000.0
|
|
|
|
|
fix 2 all npt 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0
|
|
|
|
|
fix 2 all npt 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2
|
|
|
|
|
fix 2 water npt 300.0 300.0 100.0 aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial
|
|
|
|
|
</PRE>
|
|
|
|
|
<P><B>Description:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>Perform constant NPT integration to update positions and velocities
|
|
|
|
|
each timestep for atoms in the group using a Nose/Hoover temperature
|
2007-11-15 23:29:14 +08:00
|
|
|
thermostat <A HREF = "#Hoover1">(Hoover1)</A> and Nose/Hoover pressure barostat
|
|
|
|
|
<A HREF = "#Hoover2">(Hoover2)</A>, implemented as described in
|
|
|
|
|
<A HREF = "#Melchionna">(Melchionna)</A>. P is pressure; T is temperature. This
|
|
|
|
|
creates a system trajectory consistent with the isothermal-isobaric
|
|
|
|
|
ensemble.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P>The desired temperature at each timestep is a ramped value during the
|
2007-06-26 08:03:39 +08:00
|
|
|
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).
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
|
|
|
|
<P>The atoms in the fix group are the only ones whose velocities and
|
|
|
|
|
positions are updated by the velocity/position update portion of the
|
|
|
|
|
NPT integration.
|
|
|
|
|
</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>
|
2007-02-10 05:37:30 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2006-09-22 00:22:34 +08:00
|
|
|
<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
|
2007-06-26 08:03:39 +08:00
|
|
|
the end value.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2007-07-04 03:54:12 +08:00
|
|
|
<P>Style <I>xyz</I> means couple all dimensions together when pressure is
|
|
|
|
|
computed (isotropic pressure), and dilate/contract the dimensions
|
2006-09-22 00:22:34 +08:00
|
|
|
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.
|
2007-07-04 03:54:12 +08:00
|
|
|
These styles cannot be used for a 2d simulation.
|
2006-09-22 00:22:34 +08:00
|
|
|
</P>
|
2007-07-04 03:54:12 +08:00
|
|
|
<P>For style <I>aniso</I>, all dimensions dilate/contract independently using
|
|
|
|
|
their individual pressure components as the driving forces.
|
2006-09-22 00:22:34 +08:00
|
|
|
</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
|
2007-07-04 03:54:12 +08:00
|
|
|
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>.
|
2006-09-22 00:22:34 +08:00
|
|
|
</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 and thermostat 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 and 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.
|
|
|
|
|
</P>
|
|
|
|
|
<P>For all pressure styles, the simulation box stays rectangular in
|
2007-07-04 03:57:12 +08:00
|
|
|
shape. Parinello-Rahman boundary conditions (tilted box) are not yet
|
2006-09-22 00:22:34 +08:00
|
|
|
implemented in LAMMPS.
|
|
|
|
|
</P>
|
|
|
|
|
<P>For all styles, the <I>Pdamp</I> parameter operates like the <I>Tdamp</I>
|
|
|
|
|
parameter, determining the time scale on which pressure is relaxed.
|
2007-02-10 05:37:30 +08:00
|
|
|
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>
|
|
|
|
|
<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>
|
2007-04-13 07:31:24 +08:00
|
|
|
<PRE>compute fix-ID_temp group-ID temp
|
|
|
|
|
compute fix-ID_press group-ID pressure fix-ID_temp
|
2007-02-10 05:37:30 +08:00
|
|
|
</PRE>
|
2008-01-04 08:37:21 +08:00
|
|
|
<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html">compute
|
2007-02-10 05:37:30 +08:00
|
|
|
pressure</A> commands for details. Note that the
|
2008-01-04 08:37:21 +08:00
|
|
|
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.
|
2007-02-10 05:37:30 +08:00
|
|
|
</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>
|
2008-01-18 07:46:30 +08:00
|
|
|
and <I>thermo_press</I>. This means you can change the attributes of this
|
|
|
|
|
fix's temperature or pressure via the
|
2007-02-10 05:37:30 +08:00
|
|
|
<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
|
2008-03-01 09:13:20 +08:00
|
|
|
or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
|
2007-02-10 05:37:30 +08:00
|
|
|
custom</A> command using the appropriate compute-ID.
|
|
|
|
|
It also means that changing attributes of <I>thermo_temp</I> or
|
2008-01-18 07:46:30 +08:00
|
|
|
<I>thermo_press</I> will have no effect on this fix.
|
2007-06-26 08:03:39 +08:00
|
|
|
</P>
|
2007-10-11 06:28:11 +08:00
|
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
2007-06-26 08:03:39 +08:00
|
|
|
</P>
|
|
|
|
|
<P>This fix writes the state of the Nose/Hoover thermostat and barostat
|
|
|
|
|
to <A HREF = "restart.html">binary restart files</A>. See the
|
|
|
|
|
<A HREF = "read_restart.html">read_restart</A> 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.
|
|
|
|
|
</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 thermostatting or barostatting procedure. 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>
|
2008-03-12 00:37:01 +08:00
|
|
|
<P>IMPORTANT NOTE: If both the <I>temp</I> and <I>press</I> keywords are used in a
|
|
|
|
|
single thermo_modify command (or in two separate commands), then the
|
|
|
|
|
order in which the keywords are specified is important. Note that a
|
|
|
|
|
<A HREF = "compute_pressure.html">pressure compute</A> defines its own temperature
|
|
|
|
|
compute as an argument when it is specified. The <I>temp</I> keyword will
|
|
|
|
|
override this (for the pressure compute being used by fix npt), but
|
|
|
|
|
only if the <I>temp</I> keyword comes after the <I>press</I> keyword. If the
|
|
|
|
|
<I>temp</I> keyword comes before the <I>press</I> keyword, then the new pressure
|
|
|
|
|
compute specified by the <I>press</I> keyword will be unaffected by the
|
|
|
|
|
<I>temp</I> setting.
|
|
|
|
|
</P>
|
2007-06-26 08:03:39 +08:00
|
|
|
<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
|
|
|
|
|
fix to add the energy change induced by Nose/Hoover thermostatting and
|
|
|
|
|
barostatting to the system's potential energy as part of
|
|
|
|
|
<A HREF = "thermo_style.html">thermodynamic output</A>.
|
|
|
|
|
</P>
|
2007-10-10 02:24:42 +08:00
|
|
|
<P>The potential energy change due to this fix is stored as a scalar
|
|
|
|
|
quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
|
2008-01-03 03:25:15 +08:00
|
|
|
commands</A>. The scalar value calculated by
|
|
|
|
|
this fix is "extensive", meaning it scales with the number of atoms in
|
|
|
|
|
the simulation.
|
2007-06-26 08:03:39 +08:00
|
|
|
</P>
|
|
|
|
|
<P>This fix can ramp its target temperature and 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>.
|
2006-09-22 00:22:34 +08:00
|
|
|
</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>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.
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_nph.html">fix nph</A>,
|
|
|
|
|
<A HREF = "fix_modify.html">fix_modify</A>
|
|
|
|
|
</P>
|
|
|
|
|
<P><B>Default:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>The keyword defaults are drag = 0.0 and dilate = all.
|
|
|
|
|
</P>
|
2007-11-15 23:29:14 +08:00
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<A NAME = "Hoover1"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Hoover1)</B> Hoover, Phys Rev A, 31, 1695 (1985).
|
|
|
|
|
</P>
|
|
|
|
|
<A NAME = "Hoover2"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Hoover2)</B> Hoover, Phys Rev A, 34, 2499 (1986).
|
|
|
|
|
</P>
|
|
|
|
|
<A NAME = "Melchionna"></A>
|
|
|
|
|
|
|
|
|
|
<P><B>(Melchionna)</B> Melchionna, Ciccotti, Holian, Molecular Physics, 78,
|
|
|
|
|
533-44 (1993).
|
|
|
|
|
</P>
|
2006-09-22 00:22:34 +08:00
|
|
|
</HTML>
|
