forked from lijiext/lammps
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HTML
228 lines
10 KiB
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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 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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<PRE>one or more keyword value pairs may be appended
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keyword = <I>iso</I> or <I>aniso</I> or <I>x</I> or <I>y</I> or <I>z</I> or <I>couple</I> or <I>dilate</I> or <I>modulus</I>
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<I>iso</I> or <I>aniso</I> values = Pstart Pstop Pdamp
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Pstart,Pstop = scalar external pressure at start/end of run (pressure units)
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Pdamp = pressure damping parameter (time units)
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<I>x</I> or <I>y</I> or <I>z</I> values = Pstart Pstop Pdamp
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Pstart,Pstop = external stress tensor component at start/end of run (pressure units)
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Pdamp = stress damping parameter (time units)
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<I>couple</I> = <I>none</I> or <I>xyz</I> or <I>xy</I> or <I>yz</I> or <I>xz</I>
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<I>modulus</I> value = bulk modulus of system (pressure units)
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<I>dilate</I> value = <I>all</I> or <I>partial</I>
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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 iso 0.0 0.0 1000.0
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fix 2 all press/berendsen aniso 0.0 0.0 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 within 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_nh.html">fix npt</A> or <A HREF = "fix_nh.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_nh.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_nh.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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<P>See <A HREF = "Section_howto.html#howto_16">this howto section</A> of the manual for
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a discussion of different ways to compute temperature and perform
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thermostatting and barostatting.
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</P>
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<HR>
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<P>The barostat is specified using one or more of the <I>iso</I>, <I>aniso</I>,
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<I>x</I>, <I>y</I>, <I>z</I>, and <I>couple</I> keywords. These keywords give you the
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ability to specify the 3 diagonal components of an external stress
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tensor, and to couple various of these components together so that the
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dimensions they represent are varied together during a
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constant-pressure simulation. Unlike the <A HREF = "fix_nh.html">fix npt</A> and
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<A HREF = "fix_nh.html">fix nph</A> commands, this fix cannot be used with triclinic
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(non-orthogonal) simulation boxes to control all 6 components of the
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general pressure tensor.
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</P>
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<P>The target pressures for each of the 3 diagonal components of the
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stress tensor can be specified independently via the <I>x</I>, <I>y</I>, <I>z</I>,
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keywords, which correspond to the 3 simulation box dimensions. For
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each component, the external pressure or tensor component at each
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timestep is a ramped value during the run from <I>Pstart</I> to <I>Pstop</I>.
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If a target pressure is specified for a component, then the
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corresponding box dimension will change during a simulation. For
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example, if the <I>y</I> keyword is used, the y-box length will change. A
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box dimension will not change if that component is not specified,
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although you have the option to change that dimension via the <A HREF = "fix_deform.html">fix
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deform</A> command.
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</P>
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<P>For all barostat keywords, the <I>Pdamp</I> parameter determines the time
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scale on which pressure is relaxed. For example, a value of 1000.0
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means to relax the pressure in a timespan of (roughly) 1000 time units
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(tau or fmsec or psec - see the <A HREF = "units.html">units</A> command).
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</P>
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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 (assuming the bulk modulus was a constant,
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independent of density, which it's not). The bulk modulus can be set
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via the keyword <I>modulus</I>. The <I>Pdamp</I> parameter is effectively
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multiplied by the bulk modulus, so if the pressure is relaxing faster
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than expected or desired, increasing the bulk modulus has the same
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effect as increasing <I>Pdamp</I>. The converse is also true. LAMMPS does
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not attempt to guess a correct value of the bulk modulus; it just uses
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10.0 as a default value which gives reasonable relaxation for a
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Lennard-Jones liquid, but will be way off for other materials and way
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too small for solids. Thus you should experiment to find appropriate
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values of <I>Pdamp</I> and/or the <I>modulus</I> when using this fix.
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</P>
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<HR>
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<P>The <I>couple</I> keyword allows two or three of the diagonal components of
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the pressure tensor to be "coupled" together. The value specified
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with the keyword determines which are coupled. For example, <I>xz</I>
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means the <I>Pxx</I> and <I>Pzz</I> components of the stress tensor are coupled.
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<I>Xyz</I> means all 3 diagonal components are coupled. Coupling means two
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things: the instantaneous stress will be computed as an average of the
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corresponding diagonal components, and the coupled box dimensions will
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be changed together in lockstep, meaning coupled dimensions will be
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dilated or contracted by the same percentage every timestep. The
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<I>Pstart</I>, <I>Pstop</I>, <I>Pdamp</I> parameters for any coupled dimensions must
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be identical. <I>Couple xyz</I> can be used for a 2d simulation; the <I>z</I>
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dimension is simply ignored.
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</P>
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<HR>
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<P>The <I>iso</I> and <I>aniso</I> keywords are simply shortcuts that are
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equivalent to specifying several other keywords together.
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</P>
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<P>The keyword <I>iso</I> means couple all 3 diagonal components together when
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pressure is computed (hydrostatic pressure), and dilate/contract the
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dimensions together. Using "iso Pstart Pstop Pdamp" is the same as
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specifying these 4 keywords:
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</P>
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<PRE>x Pstart Pstop Pdamp
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y Pstart Pstop Pdamp
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z Pstart Pstop Pdamp
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couple xyz
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</PRE>
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<P>The keyword <I>aniso</I> means <I>x</I>, <I>y</I>, and <I>z</I> dimensions are controlled
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independently using the <I>Pxx</I>, <I>Pyy</I>, and <I>Pzz</I> components of the
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stress tensor as the driving forces, and the specified scalar external
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pressure. Using "aniso Pstart Pstop Pdamp" is the same as specifying
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these 4 keywords:
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</P>
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<PRE>x Pstart Pstop Pdamp
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y Pstart Pstop Pdamp
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z Pstart Pstop Pdamp
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couple none
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</PRE>
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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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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 or per-atom quantities are stored by this fix for access by
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various <A HREF = "Section_howto.html#howto_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.
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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_nh.html">fix nph</A>, <A HREF = "fix_nh.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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<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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</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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