diff -Naur lammps-6Apr08/doc/Manual.html lammps-7Apr08/doc/Manual.html
--- lammps-6Apr08/doc/Manual.html	2008-01-18 14:58:10.000000000 -0700
+++ lammps-7Apr08/doc/Manual.html	2008-04-04 15:15:50.000000000 -0600
@@ -127,6 +127,8 @@
   4.14 <A HREF = "Section_howto.html#4_14">Aspherical particles</A> 
 <BR>
   4.15 <A HREF = "Section_howto.html#4_15">Output from LAMMPS</A> 
+<BR>
+  4.16 <A HREF = "Section_howto.html#4_16">Thermostatting, barostatting, and compute temperature</A> 
 <BR></UL>
 <LI><A HREF = "Section_example.html">Example problems</A> 
 
@@ -228,6 +230,8 @@
 
 
 
+
+
 </BODY>
 
 </HTML>
diff -Naur lammps-6Apr08/doc/Manual.txt lammps-7Apr08/doc/Manual.txt
--- lammps-6Apr08/doc/Manual.txt	2008-01-18 14:58:10.000000000 -0700
+++ lammps-7Apr08/doc/Manual.txt	2008-04-04 15:15:50.000000000 -0600
@@ -87,7 +87,8 @@
   4.12 "Non-orthogonal simulation boxes"_4_12 :b
   4.13 "NEMD simulations"_4_13 :b
   4.14 "Aspherical particles"_4_14 :b
-  4.15 "Output from LAMMPS"_4_15 :ule,b
+  4.15 "Output from LAMMPS"_4_15 :b
+  4.16 "Thermostatting, barostatting, and compute temperature"_4_16 :ule,b
 "Example problems"_Section_example.html :l
 "Performance & scalability"_Section_perf.html :l
 "Additional tools"_Section_tools.html :l
@@ -137,6 +138,7 @@
 :link(4_13,Section_howto.html#4_13)
 :link(4_14,Section_howto.html#4_14)
 :link(4_15,Section_howto.html#4_15)
+:link(4_16,Section_howto.html#4_16)
 
 :link(9_1,Section_errors.html#9_1)
 :link(9_2,Section_errors.html#9_2)
diff -Naur lammps-6Apr08/doc/Section_howto.html lammps-7Apr08/doc/Section_howto.html
--- lammps-6Apr08/doc/Section_howto.html	2008-03-18 15:07:29.000000000 -0600
+++ lammps-7Apr08/doc/Section_howto.html	2008-04-04 16:13:20.000000000 -0600
@@ -28,7 +28,8 @@
 4.12 <A HREF = "#4_12">Non-orthogonal simulation boxes</A><BR>
 4.13 <A HREF = "#4_13">NEMD simulations</A><BR>
 4.14 <A HREF = "#4_14">Aspherical particles</A><BR>
-4.15 <A HREF = "#4_15">Output from LAMMPS</A> <BR>
+4.15 <A HREF = "#4_15">Output from LAMMPS</A><BR>
+4.16 <A HREF = "#4_16">Thermostatting, barostatting and computing temperature</A> <BR>
 
 <P>The example input scripts included in the LAMMPS distribution and
 highlighted in <A HREF = "Section_example.html">this section</A> also show how to
@@ -1016,6 +1017,141 @@
 
 <HR>
 
+<A NAME = "4_16"></A><H4>4.16 Thermostatting, barostatting, and computing temperature 
+</H4>
+<P>Thermostatting means controlling the temperature of particles in an MD
+simulation.  Barostatting means controlling the pressure.  Since the
+pressure includes a kinetic component due to particle velocities, both
+these operations require calculation of the temperature.  Typically a
+target temperature (T) and/or pressure (P) is specified by the user,
+and the thermostat or barostat attempts to equilibrate the system to
+the requested T and/or P.
+</P>
+<P>Temperature is computed as kinetic energy divided by some number of
+degrees of freedom (and the Boltzmann constant).  Since kinetic energy
+is a function of particle velocity, there is often a need to
+distinguish between a particle's advection velocity (due to some
+aggregate motiion of particles) and its thermal velocity.  The sum of
+the two is the particle's total velocity, but the latter is often what
+is wanted to compute a temperature.
+</P>
+<P>LAMMPS has several options for computing temperatures and for using
+them in thermostatting and barostatting.
+</P>
+<P>These <A HREF = "compute.html">compute commands</A> calculate temperature.
+</P>
+<UL><LI><A HREF = "compute_temp.html">compute temp</A>
+<LI><A HREF = "compute_temp_sphere.html">compute temp/sphere</A>
+<LI><A HREF = "compute_temp_asphere.html">compute temp/asphere</A>
+<LI><A HREF = "compute_temp_com.html">compute temp/com</A>
+<LI><A HREF = "compute_temp_deform.html">compute temp/deform</A>
+<LI><A HREF = "compute_temp_partial.html">compute temp/partial</A>
+<LI><A HREF = "compute_temp_ramp.html">compute temp/ramp</A>
+<LI><A HREF = "compute_temp_region.html">compute temp/region</A> 
+</UL>
+<P>All but the first 3 calculate velocity biases (i.e. advection
+velocities) that are removed when computing the thermal temperature.
+<A HREF = "fix_temp_sphere.html">Fix temp/sphere</A> and <A HREF = "fix_temp_asphere.html">fix
+temp/asphere</A> compute kinetic energy for
+extended particles that includes rotational degrees of freedom.  They
+both allow, as an extra argument, another temperature compute that
+subtracts a velocity bias, so the translational velocity of extended
+spherical or aspherical particles can be adjusted in prescribed ways.
+</P>
+<P>Thermostatting in LAMMPS is performed by <A HREF = "fix.html">fixes</A>.  Four
+thermostatting fixes are currently available: Nose-Hoover (nvt),
+Berendsen, Langevin, and direct rescaling (temp/rescale):
+</P>
+<UL><LI><A HREF = "fix_nvt.html">fix nvt</A>
+<LI><A HREF = "fix_nvt_sphere.html">fix nvt/sphere</A>
+<LI><A HREF = "fix_nvt_asphere.html">fix nvt/asphere</A>
+<LI><A HREF = "fix_nvt_sllod.html">fix nvt/sllod</A>
+<LI><A HREF = "fix_temp_berendsen.html">fix temp/berendsen</A>
+<LI><A HREF = "fix_langevin.html">fix langevin</A>
+<LI><A HREF = "fix_temp_rescale.html">fix temp/rescale</A> 
+</UL>
+<P><A HREF = "fix_nvt.html">Fix nvt</A> only thermostats the translational velocity of
+particles.  <A HREF = "fix_nvt_sllod.html">Fix nvt/sllod</A> does as well, except
+that it subtracts out a velocity bias due to a deforming box and
+integrates the SLLOD equations of motion.  See the <A HREF = "#4_13">NEMD
+simulations</A> section of this page for further details.  <A HREF = "fix_nvt_sphere.html">Fix
+nvt/sphere</A> and <A HREF = "fix_nvt_asphere.html">fix
+nvt/asphere</A> thermostat not only translation
+velocities but also rotational velocities for spherical and aspherical
+particles.
+</P>
+<P>Any of these fixes can use temperature computes that remove bias for
+two purposes: (a) computing the current temperature to compare to the
+requested target temperature, and (b) adjusting only the thermal
+temperature component of the particle's velocities.  See the doc pages
+for the individual fixes and for the <A HREF = "fix_modify.html">fix_modify</A>
+command for instructions on how to assign a temperature compute to a
+thermostatting fix.
+</P>
+<P>IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
+they update the velocities and positions of particles due to forces
+and velocities respectively.  The other thermostat fixes only adjust
+velocities; they do NOT perform time integration.  Thus they should be
+used in conjunction with a constant NVE integration fix such as these:
+</P>
+<UL><LI><A HREF = "fix_nve.html">fix nve</A>
+<LI><A HREF = "fix_nve_sphere.html">fix nve/sphere</A>
+<LI><A HREF = "doc_fix_nve_asphere.html">fix nve/asphere</A> 
+</UL>
+<P>Barostatting in LAMMPS is also performed by <A HREF = "fix.html">fixes</A>.  Two
+barosttating methods are currently available: Nose-Hoover (npt and
+nph) and Berendsen:
+</P>
+<UL><LI><A HREF = "fix_npt.html">fix npt</A>
+<LI><A HREF = "fix_npt_sphere.html">fix npt/sphere</A>
+<LI><A HREF = "fix_npt_asphere.html">fix npt/asphere</A>
+<LI><A HREF = "fix_nph.html">fix nph</A>
+<LI><A HREF = "fix_press_berendsen.html">fix press/berendsen</A> 
+</UL>
+<P>The <A HREF = "fix_npt.html">fix npt</A> commands include a Nose-Hoover thermostat
+and barostat.  <A HREF = "fix_nph.html">Fix nph</A> is just a Nose/Hoover barostat;
+it does no thermostatting.  Both <A HREF = "fix_nph.html">fix nph</A> and <A HREF = "fix_press_berendsen.html">fix
+press/bernendsen</A> can be used in conjunction
+with any of the thermostatting fixes.
+</P>
+<P>As with the thermostats, <A HREF = "fix_npt.html">fix npt</A> and <A HREF = "fix_nph.html">fix
+nph</A> only use translational motion of the particles in
+computing T and P and performing thermo/barostatting.  <A HREF = "fix_npt_sphere.html">Fix
+npt/sphere</A> and <A HREF = "fix_npt_asphere.html">fix
+npt/asphere</A> thermo/barostat using not only
+translation velocities but also rotational velocities for spherical
+and aspherical particles.
+</P>
+<P>All of the barostatting fixes use the <A HREF = "compute_pressure.html">compute
+pressure</A> compute to calculate a current
+pressure.  The barostatting fixes can also use temperature computes
+that remove bias for the purpose of computing the current temperature
+which contributes to the current pressure.  See the doc pages for the
+individual fixes and for the <A HREF = "fix_modify.html">fix_modify</A> command for
+instructions on how to assign a temperature or pressure compute to a
+barostatting fix.
+</P>
+<P>IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods (<A HREF = "fix_npt.html">fix
+npt</A> and <A HREF = "fix_nph.html">fix nph</A>) perform time
+integration.  <A HREF = "fix_press_berendsen.html">Fix press/berendsen</A> does NOT,
+so it should be used with one of the constant NVE fixes or with one of
+the NVT fixes.
+</P>
+<P>Finally, thermodynamic output, which can be setup via the
+<A HREF = "thermo_style.html">thermo_style</A> command, often includes temperature
+and pressure values.  As explained on the doc page for the
+<A HREF = "thermo_style.html">thermo_style</A> command, the default T and P are
+setup by the thermo command itself.  They are NOT the ones associated
+with any thermostatting or barostatting fix you have defined or with
+any compute that calculates a temperature or pressure.  Thus if you
+want to view these values of T and P, you need to specify them
+explicitly via a <A HREF = "thermo_style.html">thermo_style custom</A> command.  Or
+you can use the <A HREF = "thermo_modify.html">thermo_modify</A> command to
+re-define what temperature or pressure compute is used for default
+thermodynamic output.
+</P>
+<HR>
+
 <HR>
 
 <A NAME = "Cornell"></A>
diff -Naur lammps-6Apr08/doc/Section_howto.txt lammps-7Apr08/doc/Section_howto.txt
--- lammps-6Apr08/doc/Section_howto.txt	2008-03-18 15:07:29.000000000 -0600
+++ lammps-7Apr08/doc/Section_howto.txt	2008-04-04 16:13:20.000000000 -0600
@@ -25,7 +25,8 @@
 4.12 "Non-orthogonal simulation boxes"_#4_12
 4.13 "NEMD simulations"_#4_13
 4.14 "Aspherical particles"_#4_14
-4.15 "Output from LAMMPS"_#4_15 :all(b)
+4.15 "Output from LAMMPS"_#4_15
+4.16 "Thermostatting, barostatting and computing temperature"_#4_16 :all(b)
 
 The example input scripts included in the LAMMPS distribution and
 highlighted in "this section"_Section_example.html also show how to
@@ -1006,6 +1007,141 @@
 run every: any variable: nevery: screen, log: nevery :tb(s=:)
 
 :line
+
+4.16 Thermostatting, barostatting, and computing temperature :link(4_16),h4
+
+Thermostatting means controlling the temperature of particles in an MD
+simulation.  Barostatting means controlling the pressure.  Since the
+pressure includes a kinetic component due to particle velocities, both
+these operations require calculation of the temperature.  Typically a
+target temperature (T) and/or pressure (P) is specified by the user,
+and the thermostat or barostat attempts to equilibrate the system to
+the requested T and/or P.
+
+Temperature is computed as kinetic energy divided by some number of
+degrees of freedom (and the Boltzmann constant).  Since kinetic energy
+is a function of particle velocity, there is often a need to
+distinguish between a particle's advection velocity (due to some
+aggregate motiion of particles) and its thermal velocity.  The sum of
+the two is the particle's total velocity, but the latter is often what
+is wanted to compute a temperature.
+
+LAMMPS has several options for computing temperatures and for using
+them in thermostatting and barostatting.
+
+These "compute commands"_compute.html calculate temperature.
+
+"compute temp"_compute_temp.html
+"compute temp/sphere"_compute_temp_sphere.html
+"compute temp/asphere"_compute_temp_asphere.html
+"compute temp/com"_compute_temp_com.html
+"compute temp/deform"_compute_temp_deform.html
+"compute temp/partial"_compute_temp_partial.html
+"compute temp/ramp"_compute_temp_ramp.html
+"compute temp/region"_compute_temp_region.html :ul
+
+All but the first 3 calculate velocity biases (i.e. advection
+velocities) that are removed when computing the thermal temperature.
+"Fix temp/sphere"_fix_temp_sphere.html and "fix
+temp/asphere"_fix_temp_asphere.html compute kinetic energy for
+extended particles that includes rotational degrees of freedom.  They
+both allow, as an extra argument, another temperature compute that
+subtracts a velocity bias, so the translational velocity of extended
+spherical or aspherical particles can be adjusted in prescribed ways.
+
+Thermostatting in LAMMPS is performed by "fixes"_fix.html.  Four
+thermostatting fixes are currently available: Nose-Hoover (nvt),
+Berendsen, Langevin, and direct rescaling (temp/rescale):
+
+"fix nvt"_fix_nvt.html
+"fix nvt/sphere"_fix_nvt_sphere.html
+"fix nvt/asphere"_fix_nvt_asphere.html
+"fix nvt/sllod"_fix_nvt_sllod.html
+"fix temp/berendsen"_fix_temp_berendsen.html
+"fix langevin"_fix_langevin.html
+"fix temp/rescale"_fix_temp_rescale.html :ul
+
+"Fix nvt"_fix_nvt.html only thermostats the translational velocity of
+particles.  "Fix nvt/sllod"_fix_nvt_sllod.html does as well, except
+that it subtracts out a velocity bias due to a deforming box and
+integrates the SLLOD equations of motion.  See the "NEMD
+simulations"_#4_13 section of this page for further details.  "Fix
+nvt/sphere"_fix_nvt_sphere.html and "fix
+nvt/asphere"_fix_nvt_asphere.html thermostat not only translation
+velocities but also rotational velocities for spherical and aspherical
+particles.
+
+Any of these fixes can use temperature computes that remove bias for
+two purposes: (a) computing the current temperature to compare to the
+requested target temperature, and (b) adjusting only the thermal
+temperature component of the particle's velocities.  See the doc pages
+for the individual fixes and for the "fix_modify"_fix_modify.html
+command for instructions on how to assign a temperature compute to a
+thermostatting fix.
+
+IMPORTANT NOTE: Only the nvt fixes perform time integration, meaning
+they update the velocities and positions of particles due to forces
+and velocities respectively.  The other thermostat fixes only adjust
+velocities; they do NOT perform time integration.  Thus they should be
+used in conjunction with a constant NVE integration fix such as these:
+
+"fix nve"_fix_nve.html
+"fix nve/sphere"_fix_nve_sphere.html
+"fix nve/asphere"_doc_fix_nve_asphere.html :ul
+
+Barostatting in LAMMPS is also performed by "fixes"_fix.html.  Two
+barosttating methods are currently available: Nose-Hoover (npt and
+nph) and Berendsen:
+
+"fix npt"_fix_npt.html
+"fix npt/sphere"_fix_npt_sphere.html
+"fix npt/asphere"_fix_npt_asphere.html
+"fix nph"_fix_nph.html
+"fix press/berendsen"_fix_press_berendsen.html :ul
+
+The "fix npt"_fix_npt.html commands include a Nose-Hoover thermostat
+and barostat.  "Fix nph"_fix_nph.html is just a Nose/Hoover barostat;
+it does no thermostatting.  Both "fix nph"_fix_nph.html and "fix
+press/bernendsen"_fix_press_berendsen.html can be used in conjunction
+with any of the thermostatting fixes.
+
+As with the thermostats, "fix npt"_fix_npt.html and "fix
+nph"_fix_nph.html only use translational motion of the particles in
+computing T and P and performing thermo/barostatting.  "Fix
+npt/sphere"_fix_npt_sphere.html and "fix
+npt/asphere"_fix_npt_asphere.html thermo/barostat using not only
+translation velocities but also rotational velocities for spherical
+and aspherical particles.
+
+All of the barostatting fixes use the "compute
+pressure"_compute_pressure.html compute to calculate a current
+pressure.  The barostatting fixes can also use temperature computes
+that remove bias for the purpose of computing the current temperature
+which contributes to the current pressure.  See the doc pages for the
+individual fixes and for the "fix_modify"_fix_modify.html command for
+instructions on how to assign a temperature or pressure compute to a
+barostatting fix.
+
+IMPORTANT NOTE: As with the thermostats, the Nose/Hoover methods ("fix
+npt"_fix_npt.html and "fix nph"_fix_nph.html) perform time
+integration.  "Fix press/berendsen"_fix_press_berendsen.html does NOT,
+so it should be used with one of the constant NVE fixes or with one of
+the NVT fixes.
+
+Finally, thermodynamic output, which can be setup via the
+"thermo_style"_thermo_style.html command, often includes temperature
+and pressure values.  As explained on the doc page for the
+"thermo_style"_thermo_style.html command, the default T and P are
+setup by the thermo command itself.  They are NOT the ones associated
+with any thermostatting or barostatting fix you have defined or with
+any compute that calculates a temperature or pressure.  Thus if you
+want to view these values of T and P, you need to specify them
+explicitly via a "thermo_style custom"_thermo_style.html command.  Or
+you can use the "thermo_modify"_thermo_modify.html command to
+re-define what temperature or pressure compute is used for default
+thermodynamic output.
+
+:line
 :line
 
 :link(Cornell)
diff -Naur lammps-6Apr08/doc/compute_temp.html lammps-7Apr08/doc/compute_temp.html
--- lammps-6Apr08/doc/compute_temp.html	2008-01-02 12:25:15.000000000 -0700
+++ lammps-7Apr08/doc/compute_temp.html	2008-04-04 15:15:50.000000000 -0600
@@ -58,6 +58,10 @@
 </PRE>
 <P>See the "thermo_style" command for more details.
 </P>
+<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
 <P><B>Output info:</B>
 </P>
 <P>The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/compute_temp.txt lammps-7Apr08/doc/compute_temp.txt
--- lammps-6Apr08/doc/compute_temp.txt	2008-01-02 12:25:15.000000000 -0700
+++ lammps-7Apr08/doc/compute_temp.txt	2008-04-04 15:15:50.000000000 -0600
@@ -55,6 +55,10 @@
 
 See the "thermo_style" command for more details.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
 [Output info:]
 
 The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/compute_temp_com.html lammps-7Apr08/doc/compute_temp_com.html
--- lammps-6Apr08/doc/compute_temp_com.html	2008-03-11 10:37:01.000000000 -0600
+++ lammps-7Apr08/doc/compute_temp_com.html	2008-04-04 15:15:50.000000000 -0600
@@ -65,6 +65,10 @@
 needed, the subtracted degrees-of-freedom can be altered using the
 <I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
 </P>
+<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
 <P><B>Output info:</B>
 </P>
 <P>The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/compute_temp_com.txt lammps-7Apr08/doc/compute_temp_com.txt
--- lammps-6Apr08/doc/compute_temp_com.txt	2008-03-11 10:37:01.000000000 -0600
+++ lammps-7Apr08/doc/compute_temp_com.txt	2008-04-04 15:15:50.000000000 -0600
@@ -62,6 +62,10 @@
 needed, the subtracted degrees-of-freedom can be altered using the
 {extra} option of the "compute_modify"_compute_modify.html command.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
 [Output info:]
 
 The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/compute_temp_deform.html lammps-7Apr08/doc/compute_temp_deform.html
--- lammps-6Apr08/doc/compute_temp_deform.html	2008-03-11 10:37:01.000000000 -0600
+++ lammps-7Apr08/doc/compute_temp_deform.html	2008-04-04 15:15:50.000000000 -0600
@@ -87,6 +87,10 @@
 needed, the subtracted degrees-of-freedom can be altered using the
 <I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
 </P>
+<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
 <P><B>Output info:</B>
 </P>
 <P>The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/compute_temp_deform.txt lammps-7Apr08/doc/compute_temp_deform.txt
--- lammps-6Apr08/doc/compute_temp_deform.txt	2008-03-11 10:37:01.000000000 -0600
+++ lammps-7Apr08/doc/compute_temp_deform.txt	2008-04-04 15:15:50.000000000 -0600
@@ -84,6 +84,10 @@
 needed, the subtracted degrees-of-freedom can be altered using the
 {extra} option of the "compute_modify"_compute_modify.html command.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
 [Output info:]
 
 The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/compute_temp_partial.html lammps-7Apr08/doc/compute_temp_partial.html
--- lammps-6Apr08/doc/compute_temp_partial.html	2008-03-11 10:37:01.000000000 -0600
+++ lammps-7Apr08/doc/compute_temp_partial.html	2008-04-04 15:15:50.000000000 -0600
@@ -66,6 +66,10 @@
 needed, the subtracted degrees-of-freedom can be altered using the
 <I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
 </P>
+<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
 <P><B>Output info:</B>
 </P>
 <P>The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/compute_temp_partial.txt lammps-7Apr08/doc/compute_temp_partial.txt
--- lammps-6Apr08/doc/compute_temp_partial.txt	2008-03-11 10:37:01.000000000 -0600
+++ lammps-7Apr08/doc/compute_temp_partial.txt	2008-04-04 15:15:50.000000000 -0600
@@ -63,6 +63,10 @@
 needed, the subtracted degrees-of-freedom can be altered using the
 {extra} option of the "compute_modify"_compute_modify.html command.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
 [Output info:]
 
 The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/compute_temp_ramp.html lammps-7Apr08/doc/compute_temp_ramp.html
--- lammps-6Apr08/doc/compute_temp_ramp.html	2008-03-11 10:37:01.000000000 -0600
+++ lammps-7Apr08/doc/compute_temp_ramp.html	2008-04-04 15:15:50.000000000 -0600
@@ -78,6 +78,10 @@
 needed, the subtracted degrees-of-freedom can be altered using the
 <I>extra</I> option of the <A HREF = "compute_modify.html">compute_modify</A> command.
 </P>
+<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
 <P><B>Output info:</B>
 </P>
 <P>The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/compute_temp_ramp.txt lammps-7Apr08/doc/compute_temp_ramp.txt
--- lammps-6Apr08/doc/compute_temp_ramp.txt	2008-03-11 10:37:01.000000000 -0600
+++ lammps-7Apr08/doc/compute_temp_ramp.txt	2008-04-04 15:15:50.000000000 -0600
@@ -74,6 +74,10 @@
 needed, the subtracted degrees-of-freedom can be altered using the
 {extra} option of the "compute_modify"_compute_modify.html command.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
 [Output info:]
 
 The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/compute_temp_region.html lammps-7Apr08/doc/compute_temp_region.html
--- lammps-6Apr08/doc/compute_temp_region.html	2008-03-11 12:05:41.000000000 -0600
+++ lammps-7Apr08/doc/compute_temp_region.html	2008-04-04 15:15:50.000000000 -0600
@@ -77,6 +77,10 @@
 degrees-of-freedom can be altered using the <I>extra</I> option of the
 <A HREF = "compute_modify.html">compute_modify</A> command.
 </P>
+<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
 <P><B>Output info:</B>
 </P>
 <P>The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/compute_temp_region.txt lammps-7Apr08/doc/compute_temp_region.txt
--- lammps-6Apr08/doc/compute_temp_region.txt	2008-03-11 12:05:41.000000000 -0600
+++ lammps-7Apr08/doc/compute_temp_region.txt	2008-04-04 15:15:50.000000000 -0600
@@ -74,6 +74,10 @@
 degrees-of-freedom can be altered using the {extra} option of the
 "compute_modify"_compute_modify.html command.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
 [Output info:]
 
 The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/compute_temp_sphere.html lammps-7Apr08/doc/compute_temp_sphere.html
--- lammps-6Apr08/doc/compute_temp_sphere.html	2008-03-20 18:45:02.000000000 -0600
+++ lammps-7Apr08/doc/compute_temp_sphere.html	2008-04-04 15:15:50.000000000 -0600
@@ -70,6 +70,10 @@
 be altered using the <I>extra</I> option of the
 <A HREF = "compute_modify.html">compute_modify</A> command.
 </P>
+<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
 <P><B>Output info:</B>
 </P>
 <P>The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/compute_temp_sphere.txt lammps-7Apr08/doc/compute_temp_sphere.txt
--- lammps-6Apr08/doc/compute_temp_sphere.txt	2008-03-20 18:45:02.000000000 -0600
+++ lammps-7Apr08/doc/compute_temp_sphere.txt	2008-04-04 15:15:50.000000000 -0600
@@ -67,6 +67,10 @@
 be altered using the {extra} option of the
 "compute_modify"_compute_modify.html command.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
 [Output info:]
 
 The scalar value calculated by this compute is "intensive", meaning it
diff -Naur lammps-6Apr08/doc/fix_langevin.html lammps-7Apr08/doc/fix_langevin.html
--- lammps-6Apr08/doc/fix_langevin.html	2008-03-19 16:51:12.000000000 -0600
+++ lammps-7Apr08/doc/fix_langevin.html	2008-04-04 15:15:50.000000000 -0600
@@ -85,6 +85,10 @@
 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>
+<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
 <P>The desired temperature at each timestep is a ramped value during the
 run from <I>Tstart</I> to <I>Tstop</I>.
 </P>
diff -Naur lammps-6Apr08/doc/fix_langevin.txt lammps-7Apr08/doc/fix_langevin.txt
--- lammps-6Apr08/doc/fix_langevin.txt	2008-03-19 16:51:12.000000000 -0600
+++ lammps-7Apr08/doc/fix_langevin.txt	2008-04-04 15:15:50.000000000 -0600
@@ -76,6 +76,10 @@
 controlled by another fix - e.g. by "fix nvt"_fix_nvt.html or "fix
 temp/rescale"_fix_temp_rescale.html commands.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
 The desired temperature at each timestep is a ramped value during the
 run from {Tstart} to {Tstop}.
 
diff -Naur lammps-6Apr08/doc/fix_nph.html lammps-7Apr08/doc/fix_nph.html
--- lammps-6Apr08/doc/fix_nph.html	2008-03-18 16:21:46.000000000 -0600
+++ lammps-7Apr08/doc/fix_nph.html	2008-04-04 15:15:50.000000000 -0600
@@ -81,6 +81,10 @@
 npt</A> instead of this fix, if you want to control both
 temperature and pressure via Nose/Hoover.
 </P>
+<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting and barostatting.
+</P>
 <HR>
 
 <P>The pressure can be controlled in one of several styles, as specified
diff -Naur lammps-6Apr08/doc/fix_nph.txt lammps-7Apr08/doc/fix_nph.txt
--- lammps-6Apr08/doc/fix_nph.txt	2008-03-18 16:21:46.000000000 -0600
+++ lammps-7Apr08/doc/fix_nph.txt	2008-04-04 15:15:50.000000000 -0600
@@ -72,6 +72,10 @@
 npt"_fix_npt.html instead of this fix, if you want to control both
 temperature and pressure via Nose/Hoover.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting and barostatting.
+
 :line
 
 The pressure can be controlled in one of several styles, as specified
diff -Naur lammps-6Apr08/doc/fix_npt.html lammps-7Apr08/doc/fix_npt.html
--- lammps-6Apr08/doc/fix_npt.html	2008-03-19 16:51:12.000000000 -0600
+++ lammps-7Apr08/doc/fix_npt.html	2008-04-04 15:15:50.000000000 -0600
@@ -92,6 +92,10 @@
 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>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting and barostatting.
+</P>
 <HR>
 
 <P>The pressure can be controlled in one of several styles, as specified
diff -Naur lammps-6Apr08/doc/fix_npt.txt lammps-7Apr08/doc/fix_npt.txt
--- lammps-6Apr08/doc/fix_npt.txt	2008-03-19 16:51:12.000000000 -0600
+++ lammps-7Apr08/doc/fix_npt.txt	2008-04-04 15:15:50.000000000 -0600
@@ -81,6 +81,10 @@
 by another fix - e.g. by "fix langevin"_fix_nvt.html or "fix
 temp/rescale"_fix_temp_rescale.html commands.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting and barostatting.
+
 :line
 
 The pressure can be controlled in one of several styles, as specified
diff -Naur lammps-6Apr08/doc/fix_nvt.html lammps-7Apr08/doc/fix_nvt.html
--- lammps-6Apr08/doc/fix_nvt.html	2008-03-19 16:51:12.000000000 -0600
+++ lammps-7Apr08/doc/fix_nvt.html	2008-04-04 15:15:50.000000000 -0600
@@ -75,6 +75,10 @@
 langevin</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>
 commands.
 </P>
+<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+</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:
diff -Naur lammps-6Apr08/doc/fix_nvt.txt lammps-7Apr08/doc/fix_nvt.txt
--- lammps-6Apr08/doc/fix_nvt.txt	2008-03-19 16:51:12.000000000 -0600
+++ lammps-7Apr08/doc/fix_nvt.txt	2008-04-04 15:15:50.000000000 -0600
@@ -66,6 +66,10 @@
 langevin"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html
 commands.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
 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:
diff -Naur lammps-6Apr08/doc/fix_press_berendsen.html lammps-7Apr08/doc/fix_press_berendsen.html
--- lammps-6Apr08/doc/fix_press_berendsen.html	2008-03-18 17:30:54.000000000 -0600
+++ lammps-7Apr08/doc/fix_press_berendsen.html	2008-04-04 15:15:50.000000000 -0600
@@ -73,6 +73,10 @@
 as <A HREF = "fix_nvt.html">fix nvt</A> or <A HREF = "fix_langevin.html">fix langevin</A> or <A HREF = "fix_temp_berendsen,html">fix
 temp/berendsen</A>.
 </P>
+<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting and barostatting.
+</P>
 <HR>
 
 <P>The pressure can be controlled in one of several styles, as specified
diff -Naur lammps-6Apr08/doc/fix_press_berendsen.txt lammps-7Apr08/doc/fix_press_berendsen.txt
--- lammps-6Apr08/doc/fix_press_berendsen.txt	2008-03-18 17:30:54.000000000 -0600
+++ lammps-7Apr08/doc/fix_press_berendsen.txt	2008-04-04 15:15:50.000000000 -0600
@@ -64,6 +64,10 @@
 as "fix nvt"_fix_nvt.html or "fix langevin"_fix_langevin.html or "fix
 temp/berendsen"_fix_temp_berendsen,html.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting and barostatting.
+
 :line
 
 The pressure can be controlled in one of several styles, as specified
diff -Naur lammps-6Apr08/doc/fix_temp_berendsen.html lammps-7Apr08/doc/fix_temp_berendsen.html
--- lammps-6Apr08/doc/fix_temp_berendsen.html	2008-03-19 16:51:12.000000000 -0600
+++ lammps-7Apr08/doc/fix_temp_berendsen.html	2008-04-04 15:15:50.000000000 -0600
@@ -54,6 +54,10 @@
 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>
+<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+</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:
diff -Naur lammps-6Apr08/doc/fix_temp_berendsen.txt lammps-7Apr08/doc/fix_temp_berendsen.txt
--- lammps-6Apr08/doc/fix_temp_berendsen.txt	2008-03-19 16:51:12.000000000 -0600
+++ lammps-7Apr08/doc/fix_temp_berendsen.txt	2008-04-04 15:15:50.000000000 -0600
@@ -51,6 +51,10 @@
 by another fix - e.g. by "fix nvt"_fix_nvt.html or "fix
 langevin"_fix_langevin.html commands.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
 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:
diff -Naur lammps-6Apr08/doc/fix_temp_rescale.html lammps-7Apr08/doc/fix_temp_rescale.html
--- lammps-6Apr08/doc/fix_temp_rescale.html	2008-03-19 16:51:12.000000000 -0600
+++ lammps-7Apr08/doc/fix_temp_rescale.html	2008-04-04 15:15:50.000000000 -0600
@@ -61,6 +61,10 @@
 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>
+<P>See <A HREF = "Section_howto.html#4_16">this howto section</A> of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+</P>
 <P>This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style "temp", as if one of this command had
 been issued:
diff -Naur lammps-6Apr08/doc/fix_temp_rescale.txt lammps-7Apr08/doc/fix_temp_rescale.txt
--- lammps-6Apr08/doc/fix_temp_rescale.txt	2008-03-19 16:51:12.000000000 -0600
+++ lammps-7Apr08/doc/fix_temp_rescale.txt	2008-04-04 15:15:50.000000000 -0600
@@ -58,6 +58,10 @@
 by another fix - e.g. by "fix nvt"_fix_nvt.html or "fix
 langevin"_fix_langevin.html commands.
 
+See "this howto section"_Section_howto.html#4_16 of the manual for a
+discussion of different ways to compute temperature and perform
+thermostatting.
+
 This fix computes a temperature each timestep.  To do this, the fix
 creates its own compute of style "temp", as if one of this command had
 been issued: