git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3949 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
@ -13,40 +13,18 @@
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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>fix ID group-ID npt/asphere 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
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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><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>additional thermostat and barostat related keyword/value pairs from the <A HREF = "fix_nh.html">fix npt</A> command can be appended
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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>fix 1 all npt/asphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
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fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
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fix 2 all npt/asphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
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fix 2 water npt/asphere temp 300.0 300.0 100.0 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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@ -57,6 +35,9 @@ 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>This fix differs from the <A HREF = "fix_nh.html">fix npt</A> command, which
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assumes point particles and only updates their position and velocity.
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</P>
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<P>The thermostat is applied to both the translational and rotational
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degrees of freedom for the aspherical particles, assuming a compute is
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used which calculates a temperature that includes the rotational
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@ -64,12 +45,10 @@ degrees of freedom (see below). The translational degrees of freedom
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can also have a bias velocity removed from them before thermostatting
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takes place; see the description below.
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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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<P>Additional parameters affecting the thermostat and barostat are
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specified by keywords and values documented with the <A HREF = "fix_nh.html">fix
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npt</A> command. See, for example, discussion of the <I>temp</I>,
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<I>iso</I>, <I>aniso</I>, and <I>dilate</I> keywords.
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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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@ -85,71 +64,18 @@ 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 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>For styles <I>xy</I> and <I>yz</I> and <I>xz</I>, the starting and stopping pressures
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must be the same for the two coupled dimensions and cannot be
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specified as NULL.
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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>compute fix-ID_temp all temp/asphere
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compute fix-ID_press all 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 + 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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+ underscore + "press", and the group for the new computes is "all"
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since pressure is computed for the entire system.
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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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@ -198,10 +124,8 @@ 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 cummulative energy change due to this fix is stored as a scalar
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quantity, which can be accessed by various <A HREF = "Section_howto.html#4_15">output
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commands</A>. The scalar value calculated by
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this fix is "extensive".
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<P>This fix computes the same global scalar and global vector of
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quantities as does the <A HREF = "fix_nh.html">fix npt</A> command.
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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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@ -225,21 +149,11 @@ diameter or per-particle mass.
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<P>All particles in the group must be finite-size. They cannot be point
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particles, but they can be aspherical or spherical.
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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>, <A HREF = "fix_npt_asphere.html">fix
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npt_asphere</A>, <A HREF = "fix_modify.html">fix_modify</A>
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<P><A HREF = "fix_nh.html">fix npt</A>, <A HREF = "fix_nve_asphere.html">fix nve_asphere</A>, <A HREF = "fix_nvt_asphere.html">fix
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nvt_asphere</A>, <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><B>Default:</B> none
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</P>
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</HTML>
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