2008-03-20 06:23:37 +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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2008-03-20 06:51:12 +08:00
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<H3>fix npt/sphere command
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2008-03-20 06:23:37 +08:00
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</H3>
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<P><B>Syntax:</B>
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</P>
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2010-04-03 00:51:06 +08:00
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<PRE>fix ID group-ID npt/sphere keyword value ...
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2008-03-20 06:23:37 +08:00
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</PRE>
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2010-04-03 00:51:06 +08:00
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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/sphere = 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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2008-03-20 06:23:37 +08:00
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</UL>
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<P><B>Examples:</B>
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</P>
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2010-04-03 00:51:06 +08:00
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<PRE>fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
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fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
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fix 2 all npt/sphere 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/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
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2008-03-20 06:23:37 +08:00
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</PRE>
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<P><B>Description:</B>
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</P>
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2008-03-20 06:51:12 +08:00
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<P>Perform constant NPT integration to update position, velocity, and
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angular velocity each timestep for extended spherical particles in the
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group using a Nose/Hoover temperature thermostat and Nose/Hoover
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pressure barostat. P is pressure; T is temperature. This creates a
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system trajectory consistent with the isothermal-isobaric ensemble.
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</P>
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2010-04-03 00:51:06 +08:00
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<P>This fix differs from the <A HREF = "fix_nh.html">fix npt</A> command, which
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2008-03-20 06:51:12 +08:00
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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 spherical particles, assuming a compute is
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used which calculates a temperature that includes the rotational
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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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2008-03-20 06:23:37 +08:00
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</P>
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2010-04-03 00:51:06 +08:00
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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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2008-03-20 06:23:37 +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>This fix computes a temperature and pressure each timestep. To do
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2010-04-03 00:51:06 +08:00
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this, the fix creates its own computes of style "temp/sphere" and
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2008-03-20 06:23:37 +08:00
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"pressure", as if these commands had been issued:
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</P>
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2010-04-03 00:51:06 +08:00
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<PRE>compute fix-ID_temp all temp/sphere
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compute fix-ID_press all pressure fix-ID_temp
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2008-03-20 06:23:37 +08:00
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</PRE>
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2008-03-20 06:51:12 +08:00
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<P>See the <A HREF = "compute_temp_sphere.html">compute temp/sphere</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 "all"
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since pressure is computed for the entire system.
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2008-03-20 06:23:37 +08:00
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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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2008-03-20 06:51:12 +08:00
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<P>Like other fixes that perform thermostatting, this fix can be used
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with <A HREF = "compute.html">compute commands</A> that calculate a temperature
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after removing a "bias" from the atom velocities. E.g. removing the
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center-of-mass velocity from a group of atoms or only calculating
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temperature on the x-component of velocity or only calculating
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temperature for atoms in a geometric region. This is not done by
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default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
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to assign a temperature compute to this fix that includes such a bias
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term. See the doc pages for individual <A HREF = "compute.html">compute
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commands</A> to determine which ones include a bias. In
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this case, the thermostat works in the following manner: the current
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temperature is calculated taking the bias into account, bias is
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removed from each atom, thermostatting is performed on the remaining
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thermal degrees of freedom, and the bias is added back in.
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</P>
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2008-03-20 06:23:37 +08:00
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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>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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2010-04-03 00:51:06 +08:00
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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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2008-03-20 06:23:37 +08:00
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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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2009-06-27 02:22:33 +08:00
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<P>This fix requires that atoms store torque and angular velocity (omega)
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as defined by the <A HREF = "atom_style.html">atom_style</A>. It also require they
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store either a per-particle diameter or per-type <A HREF = "shape.html">shape</A>.
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</P>
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<P>All particles in the group must be finite-size spheres. They cannot
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be point particles, nor can they be aspherical.
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2008-03-20 06:23:37 +08:00
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</P>
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<P><B>Related commands:</B>
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</P>
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2010-04-03 00:51:06 +08:00
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<P><A HREF = "fix_nh.html">fix npt</A>, <A HREF = "fix_nve_sphere.html">fix nve_sphere</A>, <A HREF = "fix_nvt_sphere.html">fix
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2008-03-20 06:51:12 +08:00
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nvt_sphere</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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2008-03-20 06:23:37 +08:00
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</P>
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2010-04-03 00:51:06 +08:00
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<P><B>Default:</B> none
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2008-03-20 06:23:37 +08:00
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</P>
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</HTML>
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