git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1590 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/fix_temp_rescale.html

@@ -20,20 +20,13 @@
 <LI>N = perform rescaling every N steps 
 <LI>Tstart,Tstop = desired temperature at start/end of run (temperature units)
 <LI>window = only rescale if temperature is outside this window (temperature units)
-<LI>fraction = rescale to target temperature by this fraction
-<LI>zero or more keyword/value pairs may be appended
-<LI>keyword = <I>region</I> or <I>partial</I> 
+<LI>fraction = rescale to target temperature by this fraction 
 </UL>
-<PRE>  <I>region</I> values = region-ID
-    region-ID = ID of region to apply rescaling to
-  <I>partial</I> values = xflag yflag zflag
-    xflag,yflag,zflag = 0/1 if the velocity component should not or should be rescaled 
-</PRE>
 <P><B>Examples:</B>
 </P>
 <PRE>fix 3 flow temp/rescale 100 1.0 1.1 0.02 0.5
-fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 region edge
-fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 partial 0 1 1 
+fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0
+fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 
 </PRE>
 <P><B>Description:</B>
 </P>
@@ -51,37 +44,27 @@ difference between the actual and desired temperature.  E.g. if
 <I>fraction</I> = 1.0, the temperature is reset to exactly the desired
 value.
 </P>
-<P>The keyword <I>region</I> applies the fix only to atoms that are in the
-specified geometric region (and in the fix group).  Since atoms can
-enter/leave a region, this test is performed each timestep.
-</P>
-<P>The keyword <I>partial</I> rescales only the specified velocity components.
-A compute of style temp/partial is used to compute the current
-temperature of just those components (see below).
-</P>
-<P>The <I>region</I> and <I>partial</I> keywords cannot currently be used together.
-</P>
-<P>A temp/rescale fix does not update the coordinates of its atoms.  It
-is normally used with a fix of style <I>nve</I> that does that.  A
-temp/rescale fix should not normally be used on atoms that also have
-their temperature controlled by another fix - e.g. a
-<A HREF = "fix_nvt.html">nvt</A> or <A HREF = "fix_langevin.html">langevin</A> fix.
+<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nvt.html">fix nvt</A> command which
+performs Nose/Hoover thermostatting AND time integration, this fix
+does NOT perform time integration.  It only modifies velocities to
+effect thermostatting.  Thus you must use a separate time integration
+fix, like <A HREF = "fix_nve.html">fix nve</A> to actually update the positions of
+atoms using the modified velocities.  Likewise, this fix should not
+normally be used on atoms that also have their temperature controlled
+by another fix - e.g. by <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
+langevin</A> commands.
 </P>
+<HR>
+
 <P>This fix computes a temperature each timestep.  To do this, the fix
-creates its own compute of style "temp" or "temp/region" or
-"temp/partial", as if one of these commands had been issued:
+creates its own compute of style "temp", as if one of this command had
+been issued:
 </P>
-<PRE>compute fix-ID_temp group-ID temp
-compute fix-ID_temp group-ID temp/region region-ID 
-compute fix-ID_temp group-ID temp/partial xflag yflag zflag 
+<PRE>compute fix-ID_temp group-ID temp 
 </PRE>
-<P>Which is used depends on whether the <I>region</I> or <I>partial</I> keywords
-were specified with the fix.  See the <A HREF = "compute_temp.html">compute
-temp</A>, <A HREF = "compute_temp_region.html">compute
-temp/region</A>, and <A HREF = "compute_temp_partial.html">compute
-temp/partial</A> commands for details.  Note
-that the ID of the new compute is the fix-ID + underscore + "temp",
-and the group for the new compute is the same as the fix group.
+<P>See the <A HREF = "compute_temp.html">compute temp</A> for details.  Note that the
+ID of the new compute is the fix-ID + underscore + "temp", and the
+group for the new compute is the same as the fix group.
 </P>
 <P>Note that this is NOT the compute used by thermodynamic output (see
 the <A HREF = "thermo_style.html">thermo_style</A> command) with ID = <I>thermo_temp</I>.
@@ -93,17 +76,31 @@ custom</A> command using the appropriate compute-ID.
 It also means that changing attributes of <I>thermo_temp</I> will have no
 effect on this fix.
 </P>
+<P>Like other fixes that perform thermostatting, this fix can be used
+with <A HREF = "compute.html">compute commands</A> that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the <A HREF = "fix_modify.html">fix_modify</A> command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual <A HREF = "compute.html">compute
+commands</A> to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
+</P>
 <P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
 </P>
 <P>No information about this fix is written to <A HREF = "restart.html">binary restart
 files</A>.
 </P>
 <P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
-fix.  You can use it to assign a <A HREF = "compute.html">compute</A> you have
-defined to this fix which will be used in its thermostatting
-procedure.  For consistency, if using the keyword <I>region</I>, the
-compute you assign should also be of style
-<A HREF = "compute_temp_region.html">temp/region</A>.
+fix.  You can use it to assign a temperature <A HREF = "compute.html">compute</A>
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above.  For consistency, the group used by
+this fix and by the compute should be the same.
 </P>
 <P>The <A HREF = "fix_modify.html">fix_modify</A> <I>energy</I> option is supported by this
 fix to add the energy change implied by a velocity rescaling to the