From bb5cfe2b70f2bab0c601ec09fdc4e2be82548ac8 Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 18 Oct 2007 22:02:20 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1060
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 doc/fix_ave_time.html  | 154 +++++++++++++++++++++++++++++------------
 doc/fix_ave_time.txt   | 145 ++++++++++++++++++++++++++------------
 doc/fix_viscosity.html |   6 ++
 doc/fix_viscosity.txt  |   6 ++
 doc/thermo_modify.html |   9 +--
 doc/thermo_modify.txt  |   9 +--
 doc/thermo_style.html  |  19 +++--
 doc/thermo_style.txt   |  19 +++--
 8 files changed, 239 insertions(+), 128 deletions(-)

diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html
index ae26a6e00a..b8c560827e 100644
--- a/doc/fix_ave_time.html
+++ b/doc/fix_ave_time.html
@@ -13,43 +13,68 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID type file 
+<PRE>fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID keyword args ... 
 </PRE>
-<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
-<LI>ave/time = style name of this fix command
-<LI>Nevery = calculate property every this many timesteps
-<LI>Nrepeat = # of times to repeat the Nevery calculation before averaging
-<LI>Nfreq = timestep frequency at which the average value is computed
-<LI>style = <I>compute</I> or <I>fix</I>
-<LI>ID = ID of compute or fix that performs the calculation
-<LI>type = 0 for scalar quantity, 1 for vector quantity, 2 for both
-<LI>file = filename to write results to (NULL = no file) 
+<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command 
+
+<LI>ave/time = style name of this fix command 
+
+<LI>Nevery = calculate property every this many timesteps 
+
+<LI>Nrepeat = # of times to repeat the Nevery calculation before averaging 
+
+<LI>Nfreq = timestep frequency at which the average value is computed 
+
+<LI>style = <I>compute</I> or <I>fix</I> 
+
+<LI>ID = ID of compute or fix that performs the calculation 
+
+<LI>zero or more keyword/arg pairs may be appended 
+
+<LI>keyword = <I>type</I> or <I>file</I> or <I>ave</I> 
+
+<PRE>  <I>type</I> arg = <I>scalar</I> or <I>vector</I> or <I>both</I>
+    scalar = single scalar value from fix or compute
+    vector = vector of values from fix or compute
+    both = both a single value and vector of values from fix or compute
+  <I>file</I> arg = filename
+    filename = file to write results to
+  <I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
+    one = output new average value every Nfreq steps
+    running = output cummulative average of all previous Nfreq steps
+    window M = output average of M most recent Nfreq steps 
+</PRE>
+
 </UL>
 <P><B>Examples:</B>
 </P>
-<PRE>fix 1 all ave/time 100 5 1000 compute myTemp 0 temp.stats
-fix 1 all ave/time 1 100 1000 fix indenter 0 temp.indent 
+<PRE>fix 1 all ave/time 100 5 1000 compute myTemp
+fix 1 all ave/time 100 5 1000 compute myTemp ave window 20
+fix 1 all ave/time 1 100 1000 fix indenter value both file temp.indent 
 </PRE>
 <P><B>Description:</B>
 </P>
 <P>Calculate one or more instantaneous quantities every few timesteps,
 and average them over a longer timescale.  The resulting averages can
-be written to a file and/or used by other <A HREF = "Section_howto.html#4_15">output
-commands</A> such as <A HREF = "thermo_style.html">thermo_style
-custom</A>.
+be used by other <A HREF = "Section_howto.html#4_15">output commands</A> such as
+<A HREF = "thermo_style.html">thermo_style custom</A>, and also written to a file.
 </P>
 <P>This fix can be used to time-average a <A HREF = "compute.html">compute</A> which
 calculates a global quantity such as a temperature or pressure or a
 <A HREF = "fix.html">fix</A> which calculates a global quantity.  Note that per-atom
-computes cannot be used with this fix; their values can be averaged by
-the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> or <A HREF = "fix_ave_atom.html">fix
+quantities cannot be averaged with this fix; their values can be
+averaged by the <A HREF = "fix_ave_spatial.html">fix ave/spatial</A> or <A HREF = "fix_ave_atom.html">fix
 ave/atom</A> commands.
 </P>
+<P>Since the calculation is performed by the compute or fix which stores
+its own "group" definition, the group specified as part of the fix
+ave/time command is ignored.
+</P>
 <P>For style <I>compute</I> the <I>ID</I> specifies a <A HREF = "compute.html">compute</A> which
 calculates the desired property.  The compute must be a "global"
 compute that calculates one or more global properties rather than a
-"per-atom" compute.  The fix must be previously defined in the input
-script.  Or it can be a compute defined by <A HREF = "thermo_style.html">thermodynamic
+"per-atom" compute.  The compute must be previously defined in the
+input script.  Or it can be a compute defined by <A HREF = "thermo_style.html">thermodynamic
 output</A> or other fixes such as <A HREF = "fix_nvt.html">fix
 nvt</A> or <A HREF = "fix_temp_rescale.html">fix temp/rescale</A>.  Users
 can write code for their own compute styles and <A HREF = "Section_modify.html">add them to
@@ -62,35 +87,61 @@ individual fix commands for details.  The fix must be previously
 defined in the input script.  Users can write code for their own fix
 styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
 </P>
-<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify how the
-property will be time-averaged.  The final averaged value(s) are
-computed every <I>Nfreq</I> timesteps.  The average is over <I>Nrepeat</I>
-values, computed in the preceeding portion of the simulation every
-<I>Nevery</I> timesteps.  Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
-values on timesteps 90,92,94,96,98,100 will be used to compute the
-final average on timestep 100.  Similary for timesteps
-190,192,194,196,198,200 on timestep 200, etc.
+<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
+timesteps the property will be evaluated in order to contribute to the
+average.  The final averaged value(s) are computed every <I>Nfreq</I>
+timesteps.  The average is over <I>Nrepeat</I> values, computed in the
+preceeding portion of the simulation every <I>Nevery</I> timesteps.
+<I>Nfreq</I> must be a multiple of <I>Nevery</I> and <I>Nevery</I> must be non-zero
+even if <I>Nrepeat</I> is 1.
 </P>
-<P>The <I>type</I> argument chooses whether the scalar and/or vector
-calculation of the compute or fix is invoked.  The former computes a
-single global value.  The latter computes N global values, where N is
-defined by the compute or fix, e.g. 6 pressure tensor components.  In
-the vector case, each of the N values is averaged independently.  If
-file output is specified, all N values are written to the file at each
-output.
+<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+timesteps 90,92,94,96,98,100 will be used to compute the final average
+on timestep 100.  Similary for timesteps 190,192,194,196,198,200 on
+timestep 200, etc.
 </P>
-<P>Since the calculation is performed by the compute or fix which stores
-its own "group" definition, the group specified for with the fix
-ave/time command is ignored.
+<HR>
+
+<P>Additional optional keywords also affect the averaging.
 </P>
-<P>If the style is <I>compute</I> and the compute calculates pressure, it will
-cause the force computations performed by LAMMPS (pair, bond, angle,
-etc) to calculate virial terms each Nevery timesteps.  If this is more
-frequent than thermodynamic output, this adds extra cost to a
-simulation.  However, if a constant pressure simulation is being run
-(<A HREF = "fix_npt.html">fix npt</A> or <A HREF = "fix_nph.html">fix nph</A>), LAMMPS is already
-calculating virial terms for the pressure every timestep.
+<P>The <I>type</I> keyword chooses whether the scalar and/or vector quantities
+produced by the compute or fix are used.  For a setting of <I>scalar</I> a
+single global value is used.  For a setting of <I>vector</I> N global
+values are used, where N is defined by the compute or fix, e.g. 6
+pressure tensor components.  For a setting of <I>both</I>, both a scalar
+the vector values are used.  When vectors are used, each of the N
+values is averaged independently.
 </P>
+<P>The <I>file</I> keyword allows a filename to be specified.  The scalar
+and/or N vector quantities are written to the file in a
+self-explanatory text format.
+</P>
+<P>The <I>ave</I> keyword determines how the scalar and/or vector values
+produced every <I>Nfreq</I> steps are averaged with each other before they
+are accessed by another output command or written to a file.
+</P>
+<P>If the <I>ave</I> setting is <I>one</I>, then the values produced on timesteps
+that are multiples of <I>Nfreq</I> are independent of each other; they are
+output as-is without further averaging.
+</P>
+<P>If the <I>ave</I> setting is <I>running</I>, then the values produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
+cummulative sense before being output.  Each output value is thus the
+average of the value on that timestep with all preceeding values.
+This running average begins when the fix is defined; it can only be
+restarted by deleting the fix via the <A HREF = "unfix.html">unfix</A> command, or
+re-defining the fix by re-specifying it.
+</P>
+<P>If the <I>ave</I> setting is <I>window</I>, then the values produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
+a moving "window" of time, so that the last M values are used to
+produce the output.  E.g. if M = 3 and Nfreq = 1000, then the output
+on step 10000 will be the average of the individual values on steps
+8000,9000,10000.  Outputs on early steps will average over less than M
+values if they are not available.
+</P>
+<HR>
+
 <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
@@ -101,13 +152,22 @@ are relevant to this fix.
 scalar and/or a vector of quantities which can be accessed by various
 <A HREF = "Section_howto.html#4_15">output commands</A>.  The values should only be
 accessed on timesteps that are multiples of <I>Nfreq</I> since that is when
-averaging is complete.
+averaging is performed.
 </P>
 <P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
 the <A HREF = "run.html">run</A> command.  This fix is not invoked during <A HREF = "minimize.html">energy
 minimization</A>.
 </P>
-<P><B>Restrictions:</B> none
+<P><B>Restrictions:</B>
+</P>
+<P>If the style is <I>compute</I> and the specified compute calculates
+pressure, it will cause the force computations performed by LAMMPS
+(pair, bond, angle, etc) to calculate virial terms each Nevery
+timesteps.  If this is more frequent than thermodynamic output, this
+adds extra cost to a simulation.  However, if a constant pressure
+simulation is being run (<A HREF = "fix_npt.html">fix npt</A> or <A HREF = "fix_nph.html">fix
+nph</A>), LAMMPS is already calculating virial terms for the
+pressure every timestep.
 </P>
 <P><B>Related commands:</B>
 </P>
@@ -116,4 +176,6 @@ ave/spatial</A>
 </P>
 <P><B>Default:</B> none
 </P>
+<P>The option defaults are style = scalar, no file output, and ave = one.
+</P>
 </HTML>
diff --git a/doc/fix_ave_time.txt b/doc/fix_ave_time.txt
index c30c8812eb..08dec5bc9d 100644
--- a/doc/fix_ave_time.txt
+++ b/doc/fix_ave_time.txt
@@ -10,43 +10,59 @@ fix ave/time command :h3
 
 [Syntax:]
 
-fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID type file :pre
+fix ID group-ID ave/time Nevery Nrepeat Nfreq style ID keyword args ... :pre
 
-ID, group-ID are documented in "fix"_fix.html command
-ave/time = style name of this fix command
-Nevery = calculate property every this many timesteps
-Nrepeat = # of times to repeat the Nevery calculation before averaging
-Nfreq = timestep frequency at which the average value is computed
-style = {compute} or {fix}
-ID = ID of compute or fix that performs the calculation
-type = 0 for scalar quantity, 1 for vector quantity, 2 for both
-file = filename to write results to (NULL = no file) :ul
+ID, group-ID are documented in "fix"_fix.html command :ulb,l
+ave/time = style name of this fix command :l
+Nevery = calculate property every this many timesteps :l
+Nrepeat = # of times to repeat the Nevery calculation before averaging :l
+Nfreq = timestep frequency at which the average value is computed :l
+style = {compute} or {fix} :l
+ID = ID of compute or fix that performs the calculation :l
+
+zero or more keyword/arg pairs may be appended :l
+keyword = {type} or {file} or {ave} :l
+  {type} arg = {scalar} or {vector} or {both}
+    scalar = single scalar value from fix or compute
+    vector = vector of values from fix or compute
+    both = both a single value and vector of values from fix or compute
+  {file} arg = filename
+    filename = file to write results to
+  {ave} args = {one} or {running} or {window M}
+    one = output new average value every Nfreq steps
+    running = output cummulative average of all previous Nfreq steps
+    window M = output average of M most recent Nfreq steps :pre
+:ule
 
 [Examples:]
 
-fix 1 all ave/time 100 5 1000 compute myTemp 0 temp.stats
-fix 1 all ave/time 1 100 1000 fix indenter 0 temp.indent :pre
+fix 1 all ave/time 100 5 1000 compute myTemp
+fix 1 all ave/time 100 5 1000 compute myTemp ave window 20
+fix 1 all ave/time 1 100 1000 fix indenter value both file temp.indent :pre
 
 [Description:]
 
 Calculate one or more instantaneous quantities every few timesteps,
 and average them over a longer timescale.  The resulting averages can
-be written to a file and/or used by other "output
-commands"_Section_howto.html#4_15 such as "thermo_style
-custom"_thermo_style.html.
+be used by other "output commands"_Section_howto.html#4_15 such as
+"thermo_style custom"_thermo_style.html, and also written to a file.
 
 This fix can be used to time-average a "compute"_compute.html which
 calculates a global quantity such as a temperature or pressure or a
 "fix"_fix.html which calculates a global quantity.  Note that per-atom
-computes cannot be used with this fix; their values can be averaged by
-the "fix ave/spatial"_fix_ave_spatial.html or "fix
+quantities cannot be averaged with this fix; their values can be
+averaged by the "fix ave/spatial"_fix_ave_spatial.html or "fix
 ave/atom"_fix_ave_atom.html commands.
 
+Since the calculation is performed by the compute or fix which stores
+its own "group" definition, the group specified as part of the fix
+ave/time command is ignored.
+
 For style {compute} the {ID} specifies a "compute"_compute.html which
 calculates the desired property.  The compute must be a "global"
 compute that calculates one or more global properties rather than a
-"per-atom" compute.  The fix must be previously defined in the input
-script.  Or it can be a compute defined by "thermodynamic
+"per-atom" compute.  The compute must be previously defined in the
+input script.  Or it can be a compute defined by "thermodynamic
 output"_thermo_style.html or other fixes such as "fix
 nvt"_fix_nvt.html or "fix temp/rescale"_fix_temp_rescale.html.  Users
 can write code for their own compute styles and "add them to
@@ -59,34 +75,60 @@ individual fix commands for details.  The fix must be previously
 defined in the input script.  Users can write code for their own fix
 styles and "add them to LAMMPS"_Section_modify.html.
 
-The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify how the
-property will be time-averaged.  The final averaged value(s) are
-computed every {Nfreq} timesteps.  The average is over {Nrepeat}
-values, computed in the preceeding portion of the simulation every
-{Nevery} timesteps.  Thus if Nevery=2, Nrepeat=6, and Nfreq=100, then
-values on timesteps 90,92,94,96,98,100 will be used to compute the
-final average on timestep 100.  Similary for timesteps
-190,192,194,196,198,200 on timestep 200, etc.
+The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
+timesteps the property will be evaluated in order to contribute to the
+average.  The final averaged value(s) are computed every {Nfreq}
+timesteps.  The average is over {Nrepeat} values, computed in the
+preceeding portion of the simulation every {Nevery} timesteps.
+{Nfreq} must be a multiple of {Nevery} and {Nevery} must be non-zero
+even if {Nrepeat} is 1.
 
-The {type} argument chooses whether the scalar and/or vector
-calculation of the compute or fix is invoked.  The former computes a
-single global value.  The latter computes N global values, where N is
-defined by the compute or fix, e.g. 6 pressure tensor components.  In
-the vector case, each of the N values is averaged independently.  If
-file output is specified, all N values are written to the file at each
-output.
+For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
+timesteps 90,92,94,96,98,100 will be used to compute the final average
+on timestep 100.  Similary for timesteps 190,192,194,196,198,200 on
+timestep 200, etc.
 
-Since the calculation is performed by the compute or fix which stores
-its own "group" definition, the group specified for with the fix
-ave/time command is ignored.
+:line
 
-If the style is {compute} and the compute calculates pressure, it will
-cause the force computations performed by LAMMPS (pair, bond, angle,
-etc) to calculate virial terms each Nevery timesteps.  If this is more
-frequent than thermodynamic output, this adds extra cost to a
-simulation.  However, if a constant pressure simulation is being run
-("fix npt"_fix_npt.html or "fix nph"_fix_nph.html), LAMMPS is already
-calculating virial terms for the pressure every timestep.
+Additional optional keywords also affect the averaging.
+
+The {type} keyword chooses whether the scalar and/or vector quantities
+produced by the compute or fix are used.  For a setting of {scalar} a
+single global value is used.  For a setting of {vector} N global
+values are used, where N is defined by the compute or fix, e.g. 6
+pressure tensor components.  For a setting of {both}, both a scalar
+the vector values are used.  When vectors are used, each of the N
+values is averaged independently.
+
+The {file} keyword allows a filename to be specified.  The scalar
+and/or N vector quantities are written to the file in a
+self-explanatory text format.
+
+The {ave} keyword determines how the scalar and/or vector values
+produced every {Nfreq} steps are averaged with each other before they
+are accessed by another output command or written to a file.
+
+If the {ave} setting is {one}, then the values produced on timesteps
+that are multiples of {Nfreq} are independent of each other; they are
+output as-is without further averaging.
+
+If the {ave} setting is {running}, then the values produced on
+timesteps that are multiples of {Nfreq} are summed and averaged in a
+cummulative sense before being output.  Each output value is thus the
+average of the value on that timestep with all preceeding values.
+This running average begins when the fix is defined; it can only be
+restarted by deleting the fix via the "unfix"_unfix.html command, or
+re-defining the fix by re-specifying it.
+
+If the {ave} setting is {window}, then the values produced on
+timesteps that are multiples of {Nfreq} are summed and averaged within
+a moving "window" of time, so that the last M values are used to
+produce the output.  E.g. if M = 3 and Nfreq = 1000, then the output
+on step 10000 will be the average of the individual values on steps
+8000,9000,10000.  Outputs on early steps will average over less than M
+values if they are not available.
+
+:line
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
@@ -98,13 +140,22 @@ Depending on the setting of the {type} parameter, this fix computes a
 scalar and/or a vector of quantities which can be accessed by various
 "output commands"_Section_howto.html#4_15.  The values should only be
 accessed on timesteps that are multiples of {Nfreq} since that is when
-averaging is complete.
+averaging is performed.
 
 No parameter of this fix can be used with the {start/stop} keywords of
 the "run"_run.html command.  This fix is not invoked during "energy
 minimization"_minimize.html.
 
-[Restrictions:] none
+[Restrictions:]
+
+If the style is {compute} and the specified compute calculates
+pressure, it will cause the force computations performed by LAMMPS
+(pair, bond, angle, etc) to calculate virial terms each Nevery
+timesteps.  If this is more frequent than thermodynamic output, this
+adds extra cost to a simulation.  However, if a constant pressure
+simulation is being run ("fix npt"_fix_npt.html or "fix
+nph"_fix_nph.html), LAMMPS is already calculating virial terms for the
+pressure every timestep.
 
 [Related commands:]
 
@@ -112,3 +163,5 @@ minimization"_minimize.html.
 ave/spatial"_fix_ave_spatial.html
 
 [Default:] none
+
+The option defaults are style = scalar, no file output, and ave = one.
diff --git a/doc/fix_viscosity.html b/doc/fix_viscosity.html
index d140b7c350..ec380a783e 100644
--- a/doc/fix_viscosity.html
+++ b/doc/fix_viscosity.html
@@ -65,6 +65,12 @@ the shear velocity profile is the viscosity of the fluid, in
 appopriate units.  See the <A HREF = "#Muller-Plathe">Muller-Plathe paper</A> for
 details.
 </P>
+<P>IMPORTANT NOTE: After equilibration, if the velocity profile you
+observe is not linear, then you are likely swapping momentum too
+frequently and are not in a regime of linear response.  In this case
+you cannot accurately infer a viscosity and should try increasing
+the Nevery parameter.
+</P>
 <P>An alternative method for calculating a viscosity is to run a NEMD
 simulation, as described in <A HREF = "Section_howto.html#4_13">this section</A> of
 the manual.  NEMD simulations deform the simmulation box via the <A HREF = "fix_deform.html">fix
diff --git a/doc/fix_viscosity.txt b/doc/fix_viscosity.txt
index 4ada5e91f8..d2549956e2 100644
--- a/doc/fix_viscosity.txt
+++ b/doc/fix_viscosity.txt
@@ -62,6 +62,12 @@ the shear velocity profile is the viscosity of the fluid, in
 appopriate units.  See the "Muller-Plathe paper"_#Muller-Plathe for
 details.
 
+IMPORTANT NOTE: After equilibration, if the velocity profile you
+observe is not linear, then you are likely swapping momentum too
+frequently and are not in a regime of linear response.  In this case
+you cannot accurately infer a viscosity and should try increasing
+the Nevery parameter.
+
 An alternative method for calculating a viscosity is to run a NEMD
 simulation, as described in "this section"_Section_howto.html#4_13 of
 the manual.  NEMD simulations deform the simmulation box via the "fix
diff --git a/doc/thermo_modify.html b/doc/thermo_modify.html
index d31b85b196..35d7991b6b 100644
--- a/doc/thermo_modify.html
+++ b/doc/thermo_modify.html
@@ -26,8 +26,6 @@
   <I>format</I> values = <I>int</I> string or <I>float</I> string or M string
     M = integer from 1 to N, where N = # of quantities being printed
     string = C-style format string
-  <I>window</I> value = N
-    N = number of previous print-outs to average over
   <I>temp</I> value = compute ID that calculates a temperature
   <I>press</I> value = compute ID that calculates a pressure
   <I>drot</I> value = compute ID that calculates rotational energy for dipolar atoms
@@ -84,10 +82,6 @@ printed in each output line, the 5th column of output in this case.
 If the format for a specific column has been set, it will take
 precedent over the <I>int</I> or <I>float</I> setting.
 </P>
-<P>The <I>window</I> keyword sets the number of previous thermodynamic screen
-outputs over which <A HREF = "thermo_style.html">thermo_style custom</A> <I>ave</I>
-quantities are averaged when printed.
-</P>
 <P>The <I>temp</I> keyword is used to determine how thermodynamic temperature
 is calculated, which is used by all thermo quantities that require a
 temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
@@ -136,8 +130,7 @@ default.
 </P>
 <P>The option defaults are lost = error, norm = yes for unit style of
 <I>lj</I>, norm = no for unit style of <I>real</I> and <I>metal</I>, flush = no,
-window = 10, temp/press/drot/grot = compute IDs defined by
-thermo_style.
+temp/press/drot/grot = compute IDs defined by thermo_style.
 </P>
 <P>The defaults for the line and format options depend on the thermo
 style.  For styles "one", "granular", and "custom" the line and format
diff --git a/doc/thermo_modify.txt b/doc/thermo_modify.txt
index 432b3a4137..7085416ebe 100644
--- a/doc/thermo_modify.txt
+++ b/doc/thermo_modify.txt
@@ -21,8 +21,6 @@ keyword = {lost} or {norm} or {flush} or {line} or {format} or {temp} or {press}
   {format} values = {int} string or {float} string or M string
     M = integer from 1 to N, where N = # of quantities being printed
     string = C-style format string
-  {window} value = N
-    N = number of previous print-outs to average over
   {temp} value = compute ID that calculates a temperature
   {press} value = compute ID that calculates a pressure
   {drot} value = compute ID that calculates rotational energy for dipolar atoms
@@ -78,10 +76,6 @@ printed in each output line, the 5th column of output in this case.
 If the format for a specific column has been set, it will take
 precedent over the {int} or {float} setting.
 
-The {window} keyword sets the number of previous thermodynamic screen
-outputs over which "thermo_style custom"_thermo_style.html {ave}
-quantities are averaged when printed.
-
 The {temp} keyword is used to determine how thermodynamic temperature
 is calculated, which is used by all thermo quantities that require a
 temperature ("temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
@@ -130,8 +124,7 @@ default.
 
 The option defaults are lost = error, norm = yes for unit style of
 {lj}, norm = no for unit style of {real} and {metal}, flush = no,
-window = 10, temp/press/drot/grot = compute IDs defined by
-thermo_style.
+temp/press/drot/grot = compute IDs defined by thermo_style.
 
 The defaults for the line and format options depend on the thermo
 style.  For styles "one", "granular", and "custom" the line and format
diff --git a/doc/thermo_style.html b/doc/thermo_style.html
index 86d7d46c1d..8946a248ad 100644
--- a/doc/thermo_style.html
+++ b/doc/thermo_style.html
@@ -30,7 +30,6 @@
                           vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
 			  pxx, pyy, pzz, pxy, pxz, pyz
                           drot, grot,
-			  tave, pave, eave, peave,
 			  c_ID, c_ID[n], f_ID, f_ID[n], v_name
       step = timestep
       atoms = # of atoms
@@ -57,7 +56,6 @@
       pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
       drot = rotational energy of dipolar atoms
       grot = rotational energy of granular atoms
-      tave, pave, eave, peave = time-averaged temp, press, etotal, pe
       c_ID = scalar quantity calculated by a compute identified by its ID
       c_ID[N] = Nth vector quantity calculated by a compute identified by its ID
       f_ID = scalar quantity calculated by a fix identified by its ID
@@ -103,6 +101,12 @@ outputting essentially any desired quantity as a simulation proceeds.
 <P>All styles except <I>custom</I> have <I>vol</I> appended to their list of
 outputs if the simulation box volume changes during the simulation.
 </P>
+<P>The values printed by the various keywords are instantaneous values,
+calculated on the current timestep.  Time-averaged quantities, which
+include values from previous timesteps, can be output by using the
+f_ID keyword and accessing a fix that does time-averaging such as the
+<A HREF = "fix_ave_time.html">fix ave/time</A> command.
+</P>
 <P>Options invoked by the <A HREF = "thermo_modify.html">thermo_modify</A> command can
 be used to set the one- or multi-line format of the print-out, the
 normalization of energy quantities (total or per-atom), and the
@@ -117,9 +121,9 @@ use the thermo_modify command after it.
 <HR>
 
 <P>Several of the thermodynamic quantities require a temperature to be
-computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
-"tave", "pave".  By default this is done by using the "thermo_temp"
-compute which is created by LAMMPS as if this command had been issued:
+computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc".  By
+default this is done by using the "thermo_temp" compute which is
+created by LAMMPS as if this command had been issued:
 </P>
 <PRE>compute thermo_temp all temp 
 </PRE>
@@ -193,11 +197,6 @@ is included in <I>evdwl</I>, <I>pe</I>, and <I>etotal</I>, and the corresponding
 correction to the pressure is included in <I>press</I> and <I>pxx</I>, <I>pyy</I>,
 etc.
 </P>
-<P>The time-averaged keywords <I>tave, pave, eave, peave</I> are averaged over
-the last N thermodynamic outputs to the screen (not the last N
-timesteps), where N is the value set by the <I>window</I> option of the
-<A HREF = "thermo_modify.html">thermo_modify</A> command (N = 10 by default).
-</P>
 <HR>
 
 <P>The <I>c_ID</I> and <I>c_ID[N]</I> keywords allow global scalar or vector
diff --git a/doc/thermo_style.txt b/doc/thermo_style.txt
index a282b4e14e..b39ddad24e 100644
--- a/doc/thermo_style.txt
+++ b/doc/thermo_style.txt
@@ -25,7 +25,6 @@ args = list of arguments for a particular style :l
                           vol, lx, ly, lz, xlo, xhi, ylo, yhi, zlo, zhi,
 			  pxx, pyy, pzz, pxy, pxz, pyz
                           drot, grot,
-			  tave, pave, eave, peave,
 			  c_ID, c_ID\[n\], f_ID, f_ID\[n\], v_name
       step = timestep
       atoms = # of atoms
@@ -52,7 +51,6 @@ args = list of arguments for a particular style :l
       pxx,pyy,pzz,pxy,pxz,pyz = 6 components of pressure tensor
       drot = rotational energy of dipolar atoms
       grot = rotational energy of granular atoms
-      tave, pave, eave, peave = time-averaged temp, press, etotal, pe
       c_ID = scalar quantity calculated by a compute identified by its ID
       c_ID\[N\] = Nth vector quantity calculated by a compute identified by its ID
       f_ID = scalar quantity calculated by a fix identified by its ID
@@ -97,6 +95,12 @@ outputting essentially any desired quantity as a simulation proceeds.
 All styles except {custom} have {vol} appended to their list of
 outputs if the simulation box volume changes during the simulation.
 
+The values printed by the various keywords are instantaneous values,
+calculated on the current timestep.  Time-averaged quantities, which
+include values from previous timesteps, can be output by using the
+f_ID keyword and accessing a fix that does time-averaging such as the
+"fix ave/time"_fix_ave_time.html command.
+
 Options invoked by the "thermo_modify"_thermo_modify.html command can
 be used to set the one- or multi-line format of the print-out, the
 normalization of energy quantities (total or per-atom), and the
@@ -111,9 +115,9 @@ use the thermo_modify command after it.
 :line
 
 Several of the thermodynamic quantities require a temperature to be
-computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc",
-"tave", "pave".  By default this is done by using the "thermo_temp"
-compute which is created by LAMMPS as if this command had been issued:
+computed: "temp", "press", "ke", "etotal", "enthalpy", "pxx etc".  By
+default this is done by using the "thermo_temp" compute which is
+created by LAMMPS as if this command had been issued:
 
 compute thermo_temp all temp :pre
 
@@ -187,11 +191,6 @@ is included in {evdwl}, {pe}, and {etotal}, and the corresponding tail
 correction to the pressure is included in {press} and {pxx}, {pyy},
 etc.
 
-The time-averaged keywords {tave, pave, eave, peave} are averaged over
-the last N thermodynamic outputs to the screen (not the last N
-timesteps), where N is the value set by the {window} option of the
-"thermo_modify"_thermo_modify.html command (N = 10 by default).
-
 :line
 
 The {c_ID} and {c_ID\[N\]} keywords allow global scalar or vector