2007-06-20 21:15:18 +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 npt/asphere 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 npt/asphere Tstart Tstop Tdamp 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>npt/asphere = style name of this fix command
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<LI>Tstart,Tstop = desired temperature at start/end of run
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<LI>Tdamp = temperature damping parameter (time units)
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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> or <I>aniso</I> args = Px_start Px_stop Py_start Py_stop Pz_start Pz_stop Pdamp
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Px_start,Px_stop,... = desired pressure in x,y,z at start/end 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 to the args
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<LI>keyword = <I>drag</I> or <I>dilate</I>
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<PRE> <I>drag</I> value = drag factor added to barostat/thermostat (0.0 = no drag)
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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 npt/asphere 300.0 300.0 100.0 xyz 0.0 0.0 1000.0
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fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0
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fix 2 all npt/asphere 300.0 300.0 100.0 xz 5.0 5.0 NULL NULL 5.0 5.0 1000.0 drag 0.2
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fix 2 water npt/asphere 300.0 300.0 100.0 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>Perform constant NPT integration to update positions, velocities,
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and angular velocity each timestep for aspherical or ellipsoidal
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particles in the group using a Nose/Hoover temperature
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thermostat and Nose/Hoover pressure barostat. P is pressure; T is
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temperature. This creates a system trajectory consistent with the
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isothermal-isobaric ensemble.
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</P>
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<P>The desired temperature at each timestep is a ramped value during the
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run from <I>Tstart</I> to <I>Tstop</I>. The <I>Tdamp</I> parameter is specified in
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time units and determines how rapidly the temperature is relaxed. For
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example, a value of 100.0 means to relax the temperature in a timespan
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of (roughly) 100 time units (tau or fmsec or psec - see the
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<A HREF = "units.html">units</A> command).
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2007-06-20 21:15:18 +08:00
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</P>
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<P>The particles in the fix group are the only ones whose velocities and
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positions are updated by the velocity/position update portion of the
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NPT integration.
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</P>
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<P>Regardless of what particles are in the fix group, a global pressure is
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computed for all particles. Similarly, when the size of the simulation
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box is changed, all particles 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 particles in the fix group are re-scaled. The latter can be
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useful for leaving the coordinates of particles 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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<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 3 dimensions together when pressure is
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computed (isotropic pressure), and dilate/contract the 3 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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</P>
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<P>For style <I>aniso</I>, all 3 dimensions dilate/contract independently
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using their individual pressure components as the 3 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.
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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 and thermostat is applied. The optional <I>drag</I> keyword will
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damp these oscillations, although it alters the Nose/Hoover equations.
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A value of 0.0 (no drag) leaves the Nose/Hoover formalism unchanged.
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A 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 and temperature is the best way to determine if the drag term
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is working. Typically a value between 0.2 to 2.0 is sufficient to
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damp 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) are not yet
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implemented in LAMMPS.
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</P>
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<P>For all styles, the <I>Pdamp</I> parameter operates like the <I>Tdamp</I>
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parameter, determining the time scale on which pressure is relaxed.
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For example, a value of 1000.0 means to relax the pressure in a
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timespan of (roughly) 1000 time units (tau or fmsec or psec - see the
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<A HREF = "units.html">units</A> command).
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</P>
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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/asphere" and
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"pressure", as if these commands had been issued:
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</P>
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<PRE>compute fix-ID_temp group-ID temp/asphere
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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_asphere.html">compute temp/asphere</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 with underscore + "temp" or
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"press" appended and the group for the new computes is the same as the
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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 thermodyanmic 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, thermo output, run start/stop, minimize info:</B>
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</P>
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<P>This fix writes the state of the Nose/Hoover thermostat and barostat
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to <A HREF = "restart.html">binary restart files</A>. See the
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<A HREF = "read_restart.html">read_restart</A> command for info on how to re-specify
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a fix in an input script that reads a restart file, so that the
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operation of the fix continues in an uninterrupted fashion.
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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 thermostatting or barostatting procedure. 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>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
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fix to add the energy change induced by Nose/Hoover thermostatting and
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barostatting to the system's potential energy as part of
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<A HREF = "thermo_style.html">thermodynamic output</A>.
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</P>
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<P>The energy change can be printed as part of thermodynamic output via
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the keyword f_ID, where ID is the fix-ID of this fix. See the
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<A HREF = "thermo_style.html">thermo_style custom</A> command for details.
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</P>
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<P>This fix can ramp its target temperature and pressure over multiple
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runs, using the <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A>
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command. See the <A HREF = "run.html">run</A> command for details of how to do
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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>This fix is part of the "asphere" package. It is only enabled if
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LAMMPS was built with that package. See the <A HREF = "Section_start.html#2_3">Making
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LAMMPS</A> section for more info.
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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>The final Tstop cannot be 0.0 since it would make the target T = 0.0
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at some timestep during the simulation which is not allowed in
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the Nose/Hoover formulation.
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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_npt.html">fix npt</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</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 drag = 0.0 and dilate = all.
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</P>
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</HTML>
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