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

doc/fix_langevin.html

@@ -27,14 +27,10 @@
 
 <LI>zero or more keyword/value pairs may be appended 
 
-keyword = <I>axes</I> or <I>scale</I> or <I>region</I>
+keyword = <I>scale</I>
-  <I>axes</I> values = xflag yflag zflag
-    xflag,yflag,zflag = 0/1 to exclude/include a dimension in the thermostat
   <I>scale</I> values = type ratio
     type = atom type (1-N)
     ratio = factor to scale the damping coefficient by
-  <I>region</I> value = region-ID
-    region-ID = ID of region to apply thermostat to
 
 </UL>
 <P><B>Examples:</B>
@@ -71,9 +67,36 @@ used to randomize the direction and magnitude of this force as
 described in <A HREF = "#Dunweg">(Dunweg)</A>, where a uniform random number is used
 (instead of a Gaussian random number) for speed.
 </P>
+<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 forces 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 velocities and
+positions of atoms using the the modified forces.  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_temp_rescale.html">fix
+temp/rescale</A> commands.
+</P>
+<HR>
+
 <P>The desired temperature at each timestep is a ramped value during the
 run from <I>Tstart</I> to <I>Tstop</I>.
 </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>The <I>damp</I> parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 100.0
 means to relax the temperature in a timespan of (roughly) 100 time
@@ -108,17 +131,6 @@ includes the particle mass in Ff, unlike fix <I>viscous</I>.  Thus the mass
 and size of different atom types should be accounted for in the choice
 of ratio values.
 </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>As noted above, fix <I>langevin</I> does not update the coordinates or
-velocities of its atoms, only the forces.  It is normally used with a
-<A HREF = "fix_nve.html">fix nve</A> that does the time integration.  Fix <I>langevin</I>
-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_temp_rescale.html">temp/rescale</A> fix.
-</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
@@ -128,10 +140,14 @@ restarts with this fix, where the simulation continues on the same as
 if no restart had taken place.  However, in a statistical sense, a
 restarted simulation should produce the same behavior.
 </P>
-<P>None of the <A HREF = "fix_modify.html">fix_modify</A> options are relevant to this
+<P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> option is supported by this
-fix.  No global scalar or vector or per-atom quantities are stored by
+fix.  You can use it to assign a temperature <A HREF = "compute.html">compute</A>
-this fix for access by various <A HREF = "Section_howto.html#4_15">output
+you have defined to this fix which will be used in its thermostatting
-commands</A>.
+procedure, as described above.  For consistency, the group used by
+this fix and by the compute should be the same.
+</P>
+<P>No global scalar or vector or per-atom quantities are stored by this
+fix for access by various <A HREF = "Section_howto.html#4_15">output commands</A>.
 </P>
 <P>This fix can ramp its target temperature over multiple runs, using the
 <I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  See the

doc/fix_langevin.txt

@@ -18,14 +18,10 @@ Tstart,Tstop = desired temperature at start/end of run (temperature units) :l
 damp = damping parameter (time units) :l
 seed = random # seed to use for white noise (positive integer) :l
 zero or more keyword/value pairs may be appended :l
-keyword = {axes} or {scale} or {region}
+keyword = {scale}
-  {axes} values = xflag yflag zflag
-    xflag,yflag,zflag = 0/1 to exclude/include a dimension in the thermostat
   {scale} values = type ratio
     type = atom type (1-N)
     ratio = factor to scale the damping coefficient by
-  {region} value = region-ID
-    region-ID = ID of region to apply thermostat to
 :ule
 
 [Examples:]
@@ -62,9 +58,36 @@ used to randomize the direction and magnitude of this force as
 described in "(Dunweg)"_#Dunweg, where a uniform random number is used
 (instead of a Gaussian random number) for speed.
 
+IMPORTANT NOTE: Unlike the "fix nvt"_fix_nvt.html command which
+performs Nose/Hoover thermostatting AND time integration, this fix
+does NOT perform time integration.  It only modifies forces to effect
+thermostatting.  Thus you must use a separate time integration fix,
+like "fix nve"_fix_nve.html to actually update the velocities and
+positions of atoms using the the modified forces.  Likewise, this fix
+should not normally be used on atoms that also have their temperature
+controlled by another fix - e.g. by "fix nvt"_fix_nvt.html or "fix
+temp/rescale"_fix_temp_rescale.html commands.
+
+:line
+
 The desired temperature at each timestep is a ramped value during the
 run from {Tstart} to {Tstop}.
 
+Like other fixes that perform thermostatting, this fix can be used
+with "compute commands"_compute.html 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 "fix_modify"_fix_modify.html command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual "compute
+commands"_compute.html 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.
+
 The {damp} parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 100.0
 means to relax the temperature in a timespan of (roughly) 100 time
@@ -99,17 +122,6 @@ includes the particle mass in Ff, unlike fix {viscous}.  Thus the mass
 and size of different atom types should be accounted for in the choice
 of ratio values.
 
-The keyword {region} 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.
-
-As noted above, fix {langevin} does not update the coordinates or
-velocities of its atoms, only the forces.  It is normally used with a
-"fix nve"_fix_nve.html that does the time integration.  Fix {langevin}
-should not normally be used on atoms that also have their temperature
-controlled by another fix - e.g. a "nvt"_fix_nvt.html or
-"temp/rescale"_fix_temp_rescale.html fix.
-
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 No information about this fix is written to "binary restart
@@ -119,10 +131,14 @@ restarts with this fix, where the simulation continues on the same as
 if no restart had taken place.  However, in a statistical sense, a
 restarted simulation should produce the same behavior.
 
-None of the "fix_modify"_fix_modify.html options are relevant to this
+The "fix_modify"_fix_modify.html {temp} option is supported by this
-fix.  No global scalar or vector or per-atom quantities are stored by
+fix.  You can use it to assign a temperature "compute"_compute.html
-this fix for access by various "output
+you have defined to this fix which will be used in its thermostatting
-commands"_Section_howto.html#4_15.
+procedure, as described above.  For consistency, the group used by
+this fix and by the compute should be the same.
+
+No global scalar or vector or per-atom quantities are stored by this
+fix for access by various "output commands"_Section_howto.html#4_15.
 
 This fix can ramp its target temperature over multiple runs, using the
 {start} and {stop} keywords of the "run"_run.html command.  See the

doc/fix_npt.html

@@ -77,6 +77,16 @@ only the atoms in the fix group are re-scaled.  The latter can be
 useful for leaving the coordinates of atoms in a solid substrate
 unchanged and controlling the pressure of a surrounding fluid.
 </P>
+<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_berendsen.html">fix temp/berendsen</A>
+command which performs thermostatting but NO time integration, this
+fix performs thermostatting/barostatting AND time integration.  Thus
+you should not use any other time integration fix, such as <A HREF = "fix_nve.html">fix
+nve</A> on atoms to which this fix is applied.  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
+langevin</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
+commands.
+</P>
 <HR>
 
 <P>The pressure can be controlled in one of several styles, as specified
@@ -151,6 +161,21 @@ custom</A> command using the appropriate compute-ID.
 It also means that changing attributes of <I>thermo_temp</I> or
 <I>thermo_press</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>This fix writes the state of the Nose/Hoover thermostat and barostat
@@ -162,11 +187,11 @@ operation of the fix continues in an uninterrupted fashion.
 <P>The <A HREF = "fix_modify.html">fix_modify</A> <I>temp</I> and <I>press</I> options are
 supported by this fix.  You can use them to assign a
 <A HREF = "compute.html">compute</A> you have defined to this fix which will be used
-in its thermostatting or barostatting procedure.  If you do this, note
+in its thermostatting or barostatting procedure, as described above.
-that the kinetic energy derived from the compute temperature should be
+If you do this, note that the kinetic energy derived from the compute
-consistent with the virial term computed using all atoms for the
+temperature should be consistent with the virial term computed using
-pressure.  LAMMPS will warn you if you choose to compute temperature
+all atoms for the pressure.  LAMMPS will warn you if you choose to
-on a subset of atoms.
+compute temperature on a subset of atoms.
 </P>
 <P>IMPORTANT NOTE: If both the <I>temp</I> and <I>press</I> keywords are used in a
 single thermo_modify command (or in two separate commands), then the

doc/fix_npt.txt

@@ -66,6 +66,16 @@ only the atoms in the fix group are re-scaled.  The latter can be
 useful for leaving the coordinates of atoms in a solid substrate
 unchanged and controlling the pressure of a surrounding fluid.
 
+IMPORTANT NOTE: Unlike the "fix temp/berendsen"_fix_berendsen.html
+command which performs thermostatting but NO time integration, this
+fix performs thermostatting/barostatting AND time integration.  Thus
+you should not use any other time integration fix, such as "fix
+nve"_fix_nve.html on atoms to which this fix is applied.  Likewise,
+this fix should not normally be used on atoms that also have their
+temperature controlled by another fix - e.g. by "fix
+langevin"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html
+commands.
+
 :line
 
 The pressure can be controlled in one of several styles, as specified
@@ -140,6 +150,21 @@ custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} or
 {thermo_press} will have no effect on this fix.
 
+Like other fixes that perform thermostatting, this fix can be used
+with "compute commands"_compute.html 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 "fix_modify"_fix_modify.html command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual "compute
+commands"_compute.html 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.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 This fix writes the state of the Nose/Hoover thermostat and barostat
@@ -151,11 +176,11 @@ operation of the fix continues in an uninterrupted fashion.
 The "fix_modify"_fix_modify.html {temp} and {press} options are
 supported by this fix.  You can use them to assign a
 "compute"_compute.html you have defined to this fix which will be used
-in its thermostatting or barostatting procedure.  If you do this, note
+in its thermostatting or barostatting procedure, as described above.
-that the kinetic energy derived from the compute temperature should be
+If you do this, note that the kinetic energy derived from the compute
-consistent with the virial term computed using all atoms for the
+temperature should be consistent with the virial term computed using
-pressure.  LAMMPS will warn you if you choose to compute temperature
+all atoms for the pressure.  LAMMPS will warn you if you choose to
-on a subset of atoms.
+compute temperature on a subset of atoms.
 
 IMPORTANT NOTE: If both the {temp} and {press} keywords are used in a
 single thermo_modify command (or in two separate commands), then the

doc/fix_nvt.html

@@ -60,6 +60,16 @@ Performing a short run and monitoring the temperature is the best way
 to determine if the drag term is working.  Typically a value between
 0.2 to 2.0 is sufficient to damp oscillations after a few periods.
 </P>
+<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_berendsen.html">fix temp/berendsen</A>
+command which performs thermostatting but NO time integration, this
+fix performs thermostatting/barostatting AND time integration.  Thus
+you should not use any other time integration fix, such as <A HREF = "fix_nve.html">fix
+nve</A> on atoms to which this fix is applied.  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
+langevin</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
+commands.
+</P>
 <P>This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style "temp", as if this command had been
 issued:
@@ -80,6 +90,21 @@ 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>This fix writes the state of the Nose/Hoover thermostat to <A HREF = "restart.html">binary
@@ -89,9 +114,10 @@ reads a restart file, so that the operation of the fix continues in an
 uninterrupted fashion.
 </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
+fix.  You can use it to assign a temperature <A HREF = "compute.html">compute</A>
-defined to this fix which will be used in its thermostatting
+you have defined to this fix which will be used in its thermostatting
-procedure.
+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 induced by Nose/Hoover thermostatting to

doc/fix_nvt.txt

@@ -51,6 +51,16 @@ Performing a short run and monitoring the temperature is the best way
 to determine if the drag term is working.  Typically a value between
 0.2 to 2.0 is sufficient to damp oscillations after a few periods.
 
+IMPORTANT NOTE: Unlike the "fix temp/berendsen"_fix_berendsen.html
+command which performs thermostatting but NO time integration, this
+fix performs thermostatting/barostatting AND time integration.  Thus
+you should not use any other time integration fix, such as "fix
+nve"_fix_nve.html on atoms to which this fix is applied.  Likewise,
+this fix should not normally be used on atoms that also have their
+temperature controlled by another fix - e.g. by "fix
+langevin"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html
+commands.
+
 This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style "temp", as if this command had been
 issued:
@@ -71,6 +81,21 @@ custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} will have no
 effect on this fix.
 
+Like other fixes that perform thermostatting, this fix can be used
+with "compute commands"_compute.html 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 "fix_modify"_fix_modify.html command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual "compute
+commands"_compute.html 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.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 This fix writes the state of the Nose/Hoover thermostat to "binary
@@ -80,9 +105,10 @@ reads a restart file, so that the operation of the fix continues in an
 uninterrupted fashion.
 
 The "fix_modify"_fix_modify.html {temp} option is supported by this
-fix.  You can use it to assign a "compute"_compute.html you have
+fix.  You can use it to assign a temperature "compute"_compute.html
-defined to this fix which will be used in its thermostatting
+you have defined to this fix which will be used in its thermostatting
-procedure.
+procedure, as described above.  For consistency, the group used by
+this fix and by the compute should be the same.
 
 The "fix_modify"_fix_modify.html {energy} option is supported by this
 fix to add the energy change induced by Nose/Hoover thermostatting to

doc/fix_temp_berendsen.html

@@ -0,0 +1,125 @@
+<HTML>
+<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> 
+</CENTER>
+
+
+
+
+
+
+<HR>
+
+<H3>fix temp/berendsen command 
+</H3>
+<P><B>Syntax:</B>
+</P>
+<PRE>fix ID group-ID temp/berendsen Tstart Tstop Tdamp 
+</PRE>
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
+<LI>temp/berendsen = style name of this fix command
+<LI>Tstart,Tstop = desired temperature at start/end of run
+<LI>Tdamp = temperature damping parameter (time units) 
+</UL>
+<P><B>Examples:</B>
+</P>
+<PRE>fix 1 all nvt 300.0 300.0 100.0
+fix 1 all nvt 300.0 300.0 100.0 drag 0.2 
+</PRE>
+<P><B>Description:</B>
+</P>
+<P>Reset the temperature of a group of atoms by using a Berendsen
+thermostat <A HREF = "#Berendsen">(Berendsen)</A>, which rescale their velocities
+every timestep.
+</P>
+<P>The desired temperature at each timestep is a ramped value during the
+run from <I>Tstart</I> to <I>Tstop</I>.  The <I>Tdamp</I> parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+<A HREF = "units.html">units</A> command).
+</P>
+<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", as if this command had been
+issued:
+</P>
+<PRE>compute fix-ID_temp group-ID temp 
+</PRE>
+<P>See the <A HREF = "compute_temp.html">compute temp</A> command 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>.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+<A HREF = "compute_modify.html">compute_modify</A> command or print this temperature
+during thermodynamic output via the <A HREF = "thermo_style.html">thermo_style
+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 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>No global scalar or vector or per-atom quantities are stored by this
+fix for access by various <A HREF = "Section_howto.html#4_15">output commands</A>.
+</P>
+<P>This fix can ramp its target temperature over multiple runs, using the
+<I>start</I> and <I>stop</I> keywords of the <A HREF = "run.html">run</A> command.  See the
+<A HREF = "run.html">run</A> command for details of how to do this.
+</P>
+<P>This fix is not invoked during <A HREF = "minimize.html">energy minimization</A>.
+</P>
+<P><B>Restrictions:</B> none
+</P>
+<P><B>Related commands:</B>
+</P>
+<P><A HREF = "fix_nve.html">fix nve</A>, <A HREF = "fix_nvt.html">fix nvt</A>, <A HREF = "fix_temp_rescale.html">fix
+temp/rescale</A>, <A HREF = "fix_langevin.html">fix langevin</A>,
+<A HREF = "fix_modify.html">fix_modify</A>, <A HREF = "compute_temp.html">compute temp</A>
+</P>
+<P><B>Default:</B> none
+</P>
+<HR>
+
+<A NAME = "Berendsen"></A>
+
+<P><B>(Berendsen)</B> Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
+Phys, 81, 3684 (1984).
+</P>
+</HTML>

doc/fix_temp_berendsen.txt

@@ -0,0 +1,120 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Section_commands.html#comm)
+
+:line
+
+fix temp/berendsen command :h3
+
+[Syntax:]
+
+fix ID group-ID temp/berendsen Tstart Tstop Tdamp :pre
+
+ID, group-ID are documented in "fix"_fix.html command
+temp/berendsen = style name of this fix command
+Tstart,Tstop = desired temperature at start/end of run
+Tdamp = temperature damping parameter (time units) :ul
+
+[Examples:]
+
+fix 1 all nvt 300.0 300.0 100.0
+fix 1 all nvt 300.0 300.0 100.0 drag 0.2 :pre
+
+[Description:]
+
+Reset the temperature of a group of atoms by using a Berendsen
+thermostat "(Berendsen)"_#Berendsen, which rescale their velocities
+every timestep.
+
+The desired temperature at each timestep is a ramped value during the
+run from {Tstart} to {Tstop}.  The {Tdamp} parameter is specified in
+time units and determines how rapidly the temperature is relaxed.  For
+example, a value of 100.0 means to relax the temperature in a timespan
+of (roughly) 100 time units (tau or fmsec or psec - see the
+"units"_units.html command).
+
+IMPORTANT NOTE: Unlike the "fix nvt"_fix_nvt.html 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 "fix nve"_fix_nve.html 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 "fix nvt"_fix_nvt.html or "fix
+langevin"_fix_langevin.html commands.
+
+:line
+
+This fix computes a temperature each timestep.  To do this, the fix
+creates its own compute of style "temp", as if this command had been
+issued:
+
+compute fix-ID_temp group-ID temp :pre
+
+See the "compute temp"_compute_temp.html command 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.
+
+Note that this is NOT the compute used by thermodynamic output (see
+the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+"compute_modify"_compute_modify.html command or print this temperature
+during thermodynamic output via the "thermo_style
+custom"_thermo_style.html command using the appropriate compute-ID.
+It also means that changing attributes of {thermo_temp} will have no
+effect on this fix.
+
+Like other fixes that perform thermostatting, this fix can be used
+with "compute commands"_compute.html 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 "fix_modify"_fix_modify.html command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual "compute
+commands"_compute.html 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.
+
+[Restart, fix_modify, output, run start/stop, minimize info:]
+
+No information about this fix is written to "binary restart
+files"_restart.html.
+
+The "fix_modify"_fix_modify.html {temp} option is supported by this
+fix.  You can use it to assign a temperature "compute"_compute.html
+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.
+
+No global scalar or vector or per-atom quantities are stored by this
+fix for access by various "output commands"_Section_howto.html#4_15.
+
+This fix can ramp its target temperature over multiple runs, using the
+{start} and {stop} keywords of the "run"_run.html command.  See the
+"run"_run.html command for details of how to do this.
+
+This fix is not invoked during "energy minimization"_minimize.html.
+
+[Restrictions:] none
+
+[Related commands:]
+
+"fix nve"_fix_nve.html, "fix nvt"_fix_nvt.html, "fix
+temp/rescale"_fix_temp_rescale.html, "fix langevin"_fix_langevin.html,
+"fix_modify"_fix_modify.html, "compute temp"_compute_temp.html
+
+[Default:] none
+
+:line
+
+:link(Berendsen)
+
+[(Berendsen)] Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem
+Phys, 81, 3684 (1984).

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>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> 
 </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
-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 
 </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
+<P>IMPORTANT NOTE: Unlike the <A HREF = "fix_nvt.html">fix nvt</A> command which
-specified geometric region (and in the fix group).  Since atoms can
+performs Nose/Hoover thermostatting AND time integration, this fix
-enter/leave a region, this test is performed each timestep.
+does NOT perform time integration.  It only modifies velocities to
-</P>
+effect thermostatting.  Thus you must use a separate time integration
-<P>The keyword <I>partial</I> rescales only the specified velocity components.
+fix, like <A HREF = "fix_nve.html">fix nve</A> to actually update the positions of
-A compute of style temp/partial is used to compute the current
+atoms using the modified velocities.  Likewise, this fix should not
-temperature of just those components (see below).
+normally be used on atoms that also have their temperature controlled
-</P>
+by another fix - e.g. by <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix
-<P>The <I>region</I> and <I>partial</I> keywords cannot currently be used together.
+langevin</A> commands.
-</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>
+<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
+creates its own compute of style "temp", as if one of this command had
-"temp/partial", as if one of these commands had been issued:
+been issued:
 </P>
-<PRE>compute fix-ID_temp group-ID temp
+<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>
-<P>Which is used depends on whether the <I>region</I> or <I>partial</I> keywords
+<P>See the <A HREF = "compute_temp.html">compute temp</A> for details.  Note that the
-were specified with the fix.  See the <A HREF = "compute_temp.html">compute
+ID of the new compute is the fix-ID + underscore + "temp", and the
-temp</A>, <A HREF = "compute_temp_region.html">compute
+group for the new compute is the same as the fix group.
-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>
 <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
+fix.  You can use it to assign a temperature <A HREF = "compute.html">compute</A>
-defined to this fix which will be used in its thermostatting
+you have defined to this fix which will be used in its thermostatting
-procedure.  For consistency, if using the keyword <I>region</I>, the
+procedure, as described above.  For consistency, the group used by
-compute you assign should also be of style
+this fix and by the compute should be the same.
-<A HREF = "compute_temp_region.html">temp/region</A>.
 </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

doc/fix_temp_rescale.txt

@@ -17,19 +17,13 @@ temp/rescale = style name of this fix command
 N = perform rescaling every N steps 
 Tstart,Tstop = desired temperature at start/end of run (temperature units)
 window = only rescale if temperature is outside this window (temperature units)
-fraction = rescale to target temperature by this fraction
+fraction = rescale to target temperature by this fraction :ul
-zero or more keyword/value pairs may be appended
-keyword = {region} or {partial} :ul
-  {region} values = region-ID
-    region-ID = ID of region to apply rescaling to
-  {partial} values = xflag yflag zflag
-    xflag,yflag,zflag = 0/1 if the velocity component should not or should be rescaled :pre
 
 [Examples:]
 
 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
-fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 partial 0 1 1 :pre
+fix 3 boundary temp/rescale 1 1.0 1.5 0.05 1.0 :pre
 
 [Description:]
 
@@ -47,37 +41,27 @@ difference between the actual and desired temperature.  E.g. if
 {fraction} = 1.0, the temperature is reset to exactly the desired
 value.
 
-The keyword {region} applies the fix only to atoms that are in the
+IMPORTANT NOTE: Unlike the "fix nvt"_fix_nvt.html command which
-specified geometric region (and in the fix group).  Since atoms can
+performs Nose/Hoover thermostatting AND time integration, this fix
-enter/leave a region, this test is performed each timestep.
+does NOT perform time integration.  It only modifies velocities to
+effect thermostatting.  Thus you must use a separate time integration
+fix, like "fix nve"_fix_nve.html 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 "fix nvt"_fix_nvt.html or "fix
+langevin"_fix_langevin.html commands.
 
-The keyword {partial} rescales only the specified velocity components.
+:line
-A compute of style temp/partial is used to compute the current
-temperature of just those components (see below).
-
-The {region} and {partial} keywords cannot currently be used together.
-
-A temp/rescale fix does not update the coordinates of its atoms.  It
-is normally used with a fix of style {nve} 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
-"nvt"_fix_nvt.html or "langevin"_fix_langevin.html fix.
 
 This fix computes a temperature each timestep.  To do this, the fix
-creates its own compute of style "temp" or "temp/region" or
+creates its own compute of style "temp", as if one of this command had
-"temp/partial", as if one of these commands had been issued:
+been issued:
 
-compute fix-ID_temp group-ID temp
+compute fix-ID_temp group-ID temp :pre
-compute fix-ID_temp group-ID temp/region region-ID 
-compute fix-ID_temp group-ID temp/partial xflag yflag zflag :pre
 
-Which is used depends on whether the {region} or {partial} keywords
+See the "compute temp"_compute_temp.html for details.  Note that the
-were specified with the fix.  See the "compute
+ID of the new compute is the fix-ID + underscore + "temp", and the
-temp"_compute_temp.html, "compute
+group for the new compute is the same as the fix group.
-temp/region"_compute_temp_region.html, and "compute
-temp/partial"_compute_temp_partial.html 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.
 
 Note that this is NOT the compute used by thermodynamic output (see
 the "thermo_style"_thermo_style.html command) with ID = {thermo_temp}.
@@ -89,17 +73,31 @@ custom"_thermo_style.html command using the appropriate compute-ID.
 It also means that changing attributes of {thermo_temp} will have no
 effect on this fix.
 
+Like other fixes that perform thermostatting, this fix can be used
+with "compute commands"_compute.html 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 "fix_modify"_fix_modify.html command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual "compute
+commands"_compute.html 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.
+
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 No information about this fix is written to "binary restart
 files"_restart.html.
 
 The "fix_modify"_fix_modify.html {temp} option is supported by this
-fix.  You can use it to assign a "compute"_compute.html you have
+fix.  You can use it to assign a temperature "compute"_compute.html
-defined to this fix which will be used in its thermostatting
+you have defined to this fix which will be used in its thermostatting
-procedure.  For consistency, if using the keyword {region}, the
+procedure, as described above.  For consistency, the group used by
-compute you assign should also be of style
+this fix and by the compute should be the same.
-"temp/region"_compute_temp_region.html.
 
 The "fix_modify"_fix_modify.html {energy} option is supported by this
 fix to add the energy change implied by a velocity rescaling to the