2008-03-19 06:21:46 +08:00
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<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>
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<HR>
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<H3>fix press/berendsen command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>fix ID group-ID press/berendsen p-style args keyword value ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>press/berendsen = style name of this fix command
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<LI>p-style = <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I> or <I>aniso</I>
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<PRE> <I>xyz</I> args = Pstart Pstop Pdamp
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Pstart,Pstop = desired pressure at start/end of run (pressure units)
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Pdamp = pressure damping parameter (time units)
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<I>xy</I> or <I>yz</I> or <I>xz</I> args = Px0 Px1 Py0 Py1 Pz0 Pz1 Pdamp
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Px0,Px1,Py0,Py1,Pz0,Pz1 = desired pressure in x,y,z at
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start/end (0/1) of run (pressure units)
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Pdamp = pressure damping parameter (time units)
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<I>aniso</I> args = Px0 Px1 Py0 Py1 Pz0 Pz1 Pdamp
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Px0,Px1,Py0,Py1,Pz0,Pz1 = desired pressure in x,y,z at
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start/end (0/1) of run (pressure units)
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Pdamp = pressure damping parameter (time units)
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</PRE>
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<LI>zero or more keyword/value pairs may be appended
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2008-03-19 06:56:54 +08:00
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<LI>keyword = <I>dilate</I> or <I>modulus</I>
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2008-03-19 06:21:46 +08:00
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2008-03-19 06:56:54 +08:00
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<PRE> <I>dilate</I> value = <I>all</I> or <I>partial</I>
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<I>modulus</I> value = bulk modulus of system (pressure units)
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2008-03-19 06:21:46 +08:00
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<PRE>fix 1 all press/berendsen xyz 0.0 0.0 1000.0
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fix 2 all press/berendsen aniso 0.0 0.0 0.0 0.0 NULL NULL 1000.0 dilate partial
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Reset the pressure of the system by using a Berendsen barostat
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<A HREF = "#Berendsen">(Berendsen)</A>, which rescales the system volume and
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(optionally) the atoms coordinates withing the simulation box every
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timestep.
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</P>
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<P>Regardless of what atoms are in the fix group, a global pressure is
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computed for all atoms. Similarly, when the size of the simulation
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box is changed, all atoms are re-scaled to new positions, unless the
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keyword <I>dilate</I> is specified with a value of <I>partial</I>, in which case
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only the atoms in the fix group are re-scaled. The latter can be
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useful for leaving the coordinates of atoms in a solid substrate
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unchanged and controlling the pressure of a surrounding fluid.
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</P>
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<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_npt.html">fix npt</A> or <A HREF = "fix_nph.html">fix
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nph</A> commands which perform Nose/Hoover barostatting AND
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time integration, this fix does NOT perform time integration. It only
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modifies the box size and atom coordinates to effect barostatting.
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Thus you must use a separate time integration fix, like <A HREF = "fix_nve.html">fix
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nve</A> or <A HREF = "fix_nvt.html">fix nvt</A> to actually update the
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positions and velocities of atoms. This fix can be used in
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conjunction with thermostatting fixes to control the temperature, such
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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
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temp/berendsen</A>.
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</P>
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<HR>
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<P>The pressure can be controlled in one of several styles, as specified
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by the <I>p-style</I> argument. In each case, the desired pressure at each
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timestep is a ramped value during the run from the starting value to
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the end value.
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</P>
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<P>Style <I>xyz</I> means couple all dimensions together when pressure is
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computed (isotropic pressure), and dilate/contract the dimensions
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together.
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</P>
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<P>Styles <I>xy</I> or <I>yz</I> or <I>xz</I> means that the 2 specified dimensions are
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coupled together, both for pressure computation and for
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dilation/contraction. The 3rd dimension dilates/contracts
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independently, using its pressure component as the driving force.
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These styles cannot be used for a 2d simulation.
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</P>
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<P>For style <I>aniso</I>, all dimensions dilate/contract independently using
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their individual pressure components as the driving forces.
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</P>
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<P>For any of the styles except <I>xyz</I>, any of the independent pressure
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components (e.g. z in <I>xy</I>, or any dimension in <I>aniso</I>) can have
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their target pressures (both start and stop values) specified as NULL.
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This means that no pressure control is applied to that dimension so
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that the box dimension remains unchanged. For a 2d simulation the z
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pressure components must be specified as NULL when using style
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<I>aniso</I>.
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</P>
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<P>In some cases (e.g. for solids) the pressure (volume) and/or
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temperature of the system can oscillate undesirably when a Nose/Hoover
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barostat is applied. The optional <I>drag</I> keyword will damp these
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oscillations, although it alters the Nose/Hoover equations. A value
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of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged. A
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non-zero value adds a drag term; the larger the value specified, the
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greater the damping effect. Performing a short run and monitoring the
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pressure is the best way to determine if the drag term is working.
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Typically a value between 0.2 to 2.0 is sufficient to damp
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oscillations after a few periods.
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</P>
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<P>For all pressure styles, the simulation box stays rectangular in
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shape. Parinello-Rahman boundary conditions (tilted box) for this fix
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are not yet implemented in LAMMPS.
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</P>
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<P>For all styles, the <I>Pdamp</I> parameter determines the time scale on
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which pressure is relaxed. For example, a value of 1000.0 means to
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relax the pressure in a timespan of (roughly) 1000 time units (tau or
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fmsec or psec - see the <A HREF = "units.html">units</A> command).
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</P>
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2008-03-19 06:56:54 +08:00
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<P>IMPORTANT NOTE: The relaxation time is actually also a function of the
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bulk modulus of the system (inverse of isothermal compressibility).
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The bulk modulus has units of pressure and is the amount of pressure
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that would need to be applied (isotropically) to reduce the volume of
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the system by a factor of 2. The bulk modulus can be set via the
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keyword <I>modulus</I>. The <I>Pdamp</I> parameter is effectively multiplied by
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the bulk modulus, so if the pressure is relaxing faster than expected
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or desired, increasing the bulk modulus has the same effect as
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increasing <I>Pdamp</I>. The converse is also true. LAMMPS does not
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attempt to guess a correct value of the bulk modulus; it just uses
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10.0 as a default value which is about right for a Lennard-Jones
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liquid, but will be way off for other materials and way too small for
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solids. Thus you should experiment to find appropriate values of
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<I>Pdamp</I> and/or the <I>modulus</I> when using this fix.
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</P>
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2008-03-19 06:21:46 +08:00
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<HR>
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<P>This fix computes a temperature and pressure each timestep. To do
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this, the fix creates its own computes of style "temp" and "pressure",
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as if these commands had been issued:
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</P>
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<PRE>compute fix-ID_temp group-ID temp
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</PRE>
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<PRE>compute fix-ID_press group-ID pressure fix-ID_temp
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</PRE>
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<P>See the <A HREF = "compute_temp.html">compute temp</A> and <A HREF = "compute_pressure.html">compute
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pressure</A> commands for details. Note that the
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IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
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+ underscore + "press", and the group for the new computes is the same
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as the fix group.
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</P>
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<P>Note that these are NOT the computes used by thermodynamic output (see
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the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>
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and <I>thermo_press</I>. This means you can change the attributes of this
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fix's temperature or pressure via the
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<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
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or pressure during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
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custom</A> command using the appropriate compute-ID.
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It also means that changing attributes of <I>thermo_temp</I> or
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<I>thermo_press</I> will have no effect on this fix.
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</P>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>.
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</P>
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<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
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supported by this fix. You can use them to assign a
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<A HREF = "compute.html">compute</A> you have defined to this fix which will be used
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in its temperature and pressure calculations. If you do this, note
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that the kinetic energy derived from the compute temperature should be
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consistent with the virial term computed using all atoms for the
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pressure. LAMMPS will warn you if you choose to compute temperature
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on a subset of atoms.
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</P>
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<P>No global scalar or vector or per-atom quantities are stored by this
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fix for access by various <A HREF = "Section_howto.html#4_15">output commands</A>.
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</P>
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<P>This fix can ramp its target pressure over multiple runs, using the
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<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command. See the
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<A HREF = "run.html">run</A> command for details of how to do this.
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</P>
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<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>Any dimension being adjusted by this fix must be periodic. A
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dimension whose target pressures are specified as NULL can be
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non-periodic or periodic.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nph.html">fix nph</A>, <A HREF = "fix_npt.html">fix
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npt</A>, <A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>,
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<A HREF = "fix_modify.html">fix_modify</A>
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</P>
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<P><B>Default:</B>
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</P>
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2008-03-19 06:56:54 +08:00
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<P>The keyword defaults are dilate = all, modulus = 10.0 in units of
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pressure for whatever <A HREF = "units.html">units</A> are defined.
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2008-03-19 06:21:46 +08:00
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</P>
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<HR>
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<A NAME = "Berendsen"></A>
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<P><B>(Berendsen)</B> Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
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Phys, 81, 3684 (1984).
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</P>
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</HTML>
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