diff --git a/doc/fix_ave_spatial.html b/doc/fix_ave_spatial.html
index 62569cd0ebd1e0a39076fbad1800e0d7b5962957..7e514e1a6f6ccbc9c1ef383d3c26d26728f478b0 100644
--- a/doc/fix_ave_spatial.html
+++ b/doc/fix_ave_spatial.html
@@ -31,8 +31,6 @@
<LI>delta = thickness of spatial layers in dim (distance units)
-<LI>file = filename to write results to (NULL = no file)
-
<LI>style = <I>density</I> or <I>compute</I> or <I>fix</I>
<PRE> <I>density</I> arg = <I>mass</I> or <I>number</I>
@@ -43,25 +41,32 @@
</PRE>
<LI>zero or more keyword/value pairs may be appended
-<PRE>keyword = <I>norm</I> or <I>units</I>
+<LI>keyword = <I>norm</I> or <I>units</I> or <I>file</I> or <I>ave</I>
+
+<PRE> <I>units</I> value = <I>box</I> or <I>lattice</I> or <I>reduced</I>
<I>norm</I> value = <I>all</I> or <I>sample</I>
- <I>units</I> value = <I>box</I> or <I>lattice</I> or <I>reduced</I>
+ <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/spatial 10000 1 10000 z lower 2.0 centro.profile compute myCentro
-fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vel.profile compute Vx norm sample
-fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 dens.profile density mass
+<PRE>fix 1 all ave/spatial 10000 1 10000 z lower 0.02 compute myCentro units reduced
+fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 compute Vx norm sample file vel.profile
+fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 density mass ave running
</PRE>
<P><B>Description:</B>
</P>
<P>Calculate one or more instantaneous per-atom quantities every few
timesteps, average them by layer in a chosen dimension and 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>.
+longer timescale. The resulting averages can 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 spatially average per-atom properties
(velocity, force) or per-atom quantities calculated by a
@@ -70,14 +75,14 @@ and/or used by other <A HREF = "Section_howto.html#4_15">output commands</A> suc
equation you define (see the <A HREF = "compute_variable_atom.html">compute
variable/atom</A> command).
</P>
-<P>The <I>density</I> styles means to simply count the number of atoms in each
-layer, either by mass or number. The <I>compute</I> style allows
-specification of a <A HREF = "compute.html">compute</A> which will be invoked to
-calculate the desired property. The compute can be previously defined
-in the input script or it can be a compute defined by a <A HREF = "dump.html">dump
-custom</A> command.
+<P>For style <I>density</I>, the number of atoms in each layer is counted,
+either by mass or by number. The <I>compute</I> style allows specification
+of a <A HREF = "compute.html">compute</A> which will be invoked to calculate the
+desired property. The compute can be previously defined in the input
+script or it can be a compute defined by a <A HREF = "dump.html">dump custom</A>
+command.
</P>
-<P>For the <I>compute</I> style, the fix ave/spatial command accesses the
+<P>For style <I>compute</I>, the fix ave/spatial command accesses the
per-atom scalar or vector values stored by the compute. Thus it must
be a "per-atom" compute with the word "atom" in its style name, rather
than a "global" compute. See the <A HREF = "fix_ave_time.html">fix ave/time</A>
@@ -95,28 +100,41 @@ per-atom compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</
Note that the <A HREF = "dump.html">dump custom</A> command can also be used to
directly output per-atom quantities calculated by a per-atom compute.
</P>
-<P>For the <I>fix</I> style, the fix ave/spatial command accesses the per-atom
+<P>For style <I>fix</I>, the fix ave/spatial command accesses the per-atom
scalar or vector values stored by another fix. The <A HREF = "fix_ave_atom.html">fix
ave/atom</A> command is an example of such a fix.
</P>
-<P>In all cases, the calculated property is averaged over atoms in each
-layer, where the layers are in a particular <I>dim</I> and have a thickness
-given by <I>delta</I>. Every Nfreq steps, when a property is calculated
-for the first time (after a previous write), the number of layers and
-the layer boundaries are computed. Thus if the simlation box changes
-size during a simulation, the number of layers and their boundaries
-may also change. Layers are defined relative to a specified <I>origin</I>,
-which may be the lower/upper edge of the box (in <I>dim</I>) or its center
-point, or a specified coordinate value. Starting at the origin,
-sufficient layers are created in both directions to completely cover
-the box. On subsequent timesteps every atom is mapped to one of the
-layers. Atoms beyond the lowermost/uppermost layer are counted in the
-first/last layer.
+<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
+timesteps the per-atom property will be evaluated in order to
+contribute to the average. The final averaged values 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>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>The per-atom property is also averaged over atoms in each layer, where
+the layers are in a particular <I>dim</I> and have a thickness given by
+<I>delta</I>. Every Nfreq steps, when an averaging is being performed and
+the per-atom property is calculated for the first time, the number of
+layers and the layer boundaries are computed. Thus if the simlation
+box changes size during a simulation, the number of layers and their
+boundaries may also change. Layers are defined relative to a
+specified <I>origin</I>, which may be the lower/upper edge of the box (in
+<I>dim</I>) or its center point, or a specified coordinate value. Starting
+at the origin, sufficient layers are created in both directions to
+completely cover the box. On subsequent timesteps every atom is
+mapped to one of the layers. Atoms beyond the lowermost/uppermost
+layer are counted in the first/last layer.
</P>
<P>For orthogonal simulation boxes, the layers are "slices" aligned with
the xyz coordinate axes. For non-orthogonal (triclinic) simulation
-boxes, the layers are "tilted slices" that align with the tilted faces
-of the box. See the <A HREF = "region.html">region prism</A> command for a
+boxes, the layers are "tilted slices" that are parallel to the tilted
+faces of the box. See the <A HREF = "region.html">region prism</A> command for a
discussion of the geometry of tilted boxes in LAMMPS. As described
there, a tilted simulation box has edge vectors a,b,c. In that
nomenclature, layers in the x dimension have faces with normals in the
@@ -124,12 +142,26 @@ nomenclature, layers in the x dimension have faces with normals in the
cross "c" direction. And layers in z have faces normal to the "a"
cross "b" direction. Note that in order to define the thickness and
position of these tilted layers in an unambiguous fashion, the <I>units</I>
-option must be set to <I>reduced</I>.
+option must be set to <I>reduced</I> when using a non-orthogonal simulation
+box, as discussed below.
+</P>
+<P>For the <I>compute</I> and <I>fix</I> keywords, the per-atom calculation
+performed by the compute or fix is on the group defined by that
+command. However, only atoms in the fix group are included in the
+layer averaging.
+</P>
+<P>Note that some computes perform costly calculations, involving the
+creation or use of neighbor lists. If the compute is invoked too
+often by fix ave/spatial, it can slow down a simulation.
+</P>
+<HR>
+
+<P>Additional optional keywords also affect the operation of this fix.
</P>
<P>The <I>units</I> keyword determines the meaning of the distance units used
for the layer thickness <I>delta</I> and for <I>origin</I> if it is a coordinate
value. For orthogonal simulation boxes, any of the 3 options may be
-used. For non-orthongal (triclinic) simulation boxes, only the
+used. For non-orthogonal (triclinic) simulation boxes, only the
<I>reduced</I> option may be used.
</P>
<P>A <I>box</I> value selects standard distance units as defined by the
@@ -149,52 +181,64 @@ the lower "b" cross "c" plane of the simulation box and an <I>origin</I> of
A <I>delta</I> value of 0.1 means there will be 10 layers from 0.0 to 1.0,
regardless of the current size or shape of the simulation box.
</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>
-<P>The <I>norm</I> keyword also affects how time-averaging is done. For an
-<I>all</I> setting, a layer quantity is summed over all atoms in all
-Nfreq/Nevery samples, as is the count of atoms in the layer. The
-printed value for the layer is Total-quantity / Total-count.
-In other words it is an average over the entire Nfreq timescale.
+<P>The <I>norm</I> keyword affects how time-averaging is done within for the
+output produced every <I>Nfreq</I> timesteps. For an <I>all</I> setting, a
+layer quantity is summed over all atoms in all <I>Nrepeat</I> samples, as
+is the count of atoms in the layer. The printed value for the layer
+is Total-quantity / Total-count. In other words it is an average over
+the entire <I>Nfreq</I> timescale.
</P>
<P>For a <I>sample</I> setting, the quantity is summed over atoms for only a
single sample, as is the count, and a "average sample value" is
computed, i.e. Sample-quantity / Sample-count. The printed value for
-the layer is the average of the M "average sample values", where M =
-Nfreq/Nevery. In other words it is an average of an average.
-</P>
-<P>If file output is specified, each time info is written to the file, it
-is in the following format. A line with the timestep and number of
-layers is written. Then one line per layer is written, containing the
-layer ID (1-N), the coordinate of the center of the layer, the number
-of atoms in the layer, and one or more calculated values. The number
-of atoms and the value(s) are average quantities. If the value of the
-<I>units</I> keyword is <I>box</I> or <I>lattice</I>, the "coord" is printed in box
-units. If the value of the <I>units</I> keyword is <I>reduced</I>, the "coord"
-is printed in reduced units (0-1).
-</P>
-<P>If the <I>density</I> keyword is used, or the <I>compute</I> or <I>fix</I> keyword
-with a compute/fix that calculates a single quantity per atom, then a
-single value will be printed for each layer. If the <I>compute</I> or
-<I>fix</I> keyword is used with a compute/fix that calculates N quantities
-per atom, then N values per line will be written, each of them
-averaged independently.
-</P>
-<P>For the <I>compute</I> and <I>fix</I> keywords, the calculation performed by the
-compute or fix is on the group defined by the that command. However,
-only atoms in the fix group are included in the layer averaging.
-</P>
-<P>Note that some computes perform costly calculations, involving use of
-or creation of neighbor lists. If the compute is invoked too often by
-fix ave/spatial, it can slow down a simulation.
+the layer is the average of the <I>Nrepeat</I> "average sample values", In
+other words it is an average of an average.
</P>
+<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
+timesteps, layer info will be written to a text file in the following
+format. A line with the timestep and number of layers is written.
+Then one line per layer is written, containing the layer ID (1-N), the
+coordinate of the center of the layer, the number of atoms in the
+layer, and one or more calculated values. The number of atoms and the
+value(s) are average quantities. If the value of the <I>units</I> keyword
+is <I>box</I> or <I>lattice</I>, the "coord" is printed in box units. If the
+value of the <I>units</I> keyword is <I>reduced</I>, the "coord" is printed in
+reduced units (0-1).
+</P>
+<P>If the style is <I>density</I>, or the style is <I>compute</I> or <I>fix</I> with a
+compute/fix that calculates a single quantity per atom, then a single
+value will be printed for each layer. If the style is <I>compute</I> or
+<I>fix</I> with a compute/fix that calculates N quantities per atom, then N
+values per line will be written, each of them averaged independently.
+</P>
+<P>The <I>ave</I> keyword determines how the layer values produced every
+<I>Nfreq</I> steps are averaged with layer values produced on previous
+steps that were multiples of <I>Nfreq</I>, 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 layuer 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 layer values produced on
+timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
+cummulative sense before being output. Each output layer value is
+thus the average of the layer value produced on that timestep with all
+preceeding values for the same layer. 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 layer 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 for the same
+layer 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
+layer 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
@@ -224,6 +268,7 @@ minimization</A>.
</P>
<P><B>Default:</B>
</P>
-<P>The option defaults are norm = all and units = lattice.
+<P>The option defaults are units = lattice, norm = all, no file output,
+and ave = one.
</P>
</HTML>
diff --git a/doc/fix_ave_spatial.txt b/doc/fix_ave_spatial.txt
index 8ce58792d8c75c97bc7b1da8e3ad3165fa24ab3a..a84b9c92451eba21ca9fca8bffeda7c3beec5c2d 100644
--- a/doc/fix_ave_spatial.txt
+++ b/doc/fix_ave_spatial.txt
@@ -20,7 +20,6 @@ Nfreq = timestep frequency at which the average value is computed :l
dim = {x} or {y} or {z} :l
origin = {lower} or {center} or {upper} or coordinate value (distance units) :l
delta = thickness of spatial layers in dim (distance units) :l
-file = filename to write results to (NULL = no file) :l
style = {density} or {compute} or {fix} :l
{density} arg = {mass} or {number}
{mass} = compute mass density
@@ -28,24 +27,30 @@ style = {density} or {compute} or {fix} :l
{compute} arg = compute-ID that stores or calculates per-atom quantities
{fix} arg = fix-ID that stores or calculates per-atom quantities :pre
zero or more keyword/value pairs may be appended :l
-keyword = {norm} or {units}
+keyword = {norm} or {units} or {file} or {ave} :l
+ {units} value = {box} or {lattice} or {reduced}
{norm} value = {all} or {sample}
- {units} value = {box} or {lattice} or {reduced} :pre
+ {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/spatial 10000 1 10000 z lower 2.0 centro.profile compute myCentro
-fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vel.profile compute Vx norm sample
-fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 dens.profile density mass :pre
+fix 1 all ave/spatial 10000 1 10000 z lower 0.02 compute myCentro units reduced
+fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 compute Vx norm sample file vel.profile
+fix 1 flow ave/spatial 100 5 1000 y 0.0 2.5 density mass ave running :pre
[Description:]
Calculate one or more instantaneous per-atom quantities every few
timesteps, average them by layer in a chosen dimension and 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.
+longer timescale. The resulting averages can 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 spatially average per-atom properties
(velocity, force) or per-atom quantities calculated by a
@@ -54,14 +59,14 @@ This fix can be used to spatially average per-atom properties
equation you define (see the "compute
variable/atom"_compute_variable_atom.html command).
-The {density} styles means to simply count the number of atoms in each
-layer, either by mass or number. The {compute} style allows
-specification of a "compute"_compute.html which will be invoked to
-calculate the desired property. The compute can be previously defined
-in the input script or it can be a compute defined by a "dump
-custom"_dump.html command.
+For style {density}, the number of atoms in each layer is counted,
+either by mass or by number. The {compute} style allows specification
+of a "compute"_compute.html which will be invoked to calculate the
+desired property. The compute can be previously defined in the input
+script or it can be a compute defined by a "dump custom"_dump.html
+command.
-For the {compute} style, the fix ave/spatial command accesses the
+For style {compute}, the fix ave/spatial command accesses the
per-atom scalar or vector values stored by the compute. Thus it must
be a "per-atom" compute with the word "atom" in its style name, rather
than a "global" compute. See the "fix ave/time"_fix_ave_time.html
@@ -79,28 +84,41 @@ per-atom compute styles and "add them to LAMMPS"_Section_modify.html.
Note that the "dump custom"_dump.html command can also be used to
directly output per-atom quantities calculated by a per-atom compute.
-For the {fix} style, the fix ave/spatial command accesses the per-atom
+For style {fix}, the fix ave/spatial command accesses the per-atom
scalar or vector values stored by another fix. The "fix
ave/atom"_fix_ave_atom.html command is an example of such a fix.
-In all cases, the calculated property is averaged over atoms in each
-layer, where the layers are in a particular {dim} and have a thickness
-given by {delta}. Every Nfreq steps, when a property is calculated
-for the first time (after a previous write), the number of layers and
-the layer boundaries are computed. Thus if the simlation box changes
-size during a simulation, the number of layers and their boundaries
-may also change. Layers are defined relative to a specified {origin},
-which may be the lower/upper edge of the box (in {dim}) or its center
-point, or a specified coordinate value. Starting at the origin,
-sufficient layers are created in both directions to completely cover
-the box. On subsequent timesteps every atom is mapped to one of the
-layers. Atoms beyond the lowermost/uppermost layer are counted in the
-first/last layer.
+The {Nevery}, {Nrepeat}, and {Nfreq} arguments specify on what
+timesteps the per-atom property will be evaluated in order to
+contribute to the average. The final averaged values 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.
+
+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.
+
+The per-atom property is also averaged over atoms in each layer, where
+the layers are in a particular {dim} and have a thickness given by
+{delta}. Every Nfreq steps, when an averaging is being performed and
+the per-atom property is calculated for the first time, the number of
+layers and the layer boundaries are computed. Thus if the simlation
+box changes size during a simulation, the number of layers and their
+boundaries may also change. Layers are defined relative to a
+specified {origin}, which may be the lower/upper edge of the box (in
+{dim}) or its center point, or a specified coordinate value. Starting
+at the origin, sufficient layers are created in both directions to
+completely cover the box. On subsequent timesteps every atom is
+mapped to one of the layers. Atoms beyond the lowermost/uppermost
+layer are counted in the first/last layer.
For orthogonal simulation boxes, the layers are "slices" aligned with
the xyz coordinate axes. For non-orthogonal (triclinic) simulation
-boxes, the layers are "tilted slices" that align with the tilted faces
-of the box. See the "region prism"_region.html command for a
+boxes, the layers are "tilted slices" that are parallel to the tilted
+faces of the box. See the "region prism"_region.html command for a
discussion of the geometry of tilted boxes in LAMMPS. As described
there, a tilted simulation box has edge vectors a,b,c. In that
nomenclature, layers in the x dimension have faces with normals in the
@@ -108,12 +126,26 @@ nomenclature, layers in the x dimension have faces with normals in the
cross "c" direction. And layers in z have faces normal to the "a"
cross "b" direction. Note that in order to define the thickness and
position of these tilted layers in an unambiguous fashion, the {units}
-option must be set to {reduced}.
+option must be set to {reduced} when using a non-orthogonal simulation
+box, as discussed below.
+
+For the {compute} and {fix} keywords, the per-atom calculation
+performed by the compute or fix is on the group defined by that
+command. However, only atoms in the fix group are included in the
+layer averaging.
+
+Note that some computes perform costly calculations, involving the
+creation or use of neighbor lists. If the compute is invoked too
+often by fix ave/spatial, it can slow down a simulation.
+
+:line
+
+Additional optional keywords also affect the operation of this fix.
The {units} keyword determines the meaning of the distance units used
for the layer thickness {delta} and for {origin} if it is a coordinate
value. For orthogonal simulation boxes, any of the 3 options may be
-used. For non-orthongal (triclinic) simulation boxes, only the
+used. For non-orthogonal (triclinic) simulation boxes, only the
{reduced} option may be used.
A {box} value selects standard distance units as defined by the
@@ -133,51 +165,63 @@ the lower "b" cross "c" plane of the simulation box and an {origin} of
A {delta} value of 0.1 means there will be 10 layers from 0.0 to 1.0,
regardless of the current size or shape of the simulation box.
-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 {norm} keyword also affects how time-averaging is done. For an
-{all} setting, a layer quantity is summed over all atoms in all
-Nfreq/Nevery samples, as is the count of atoms in the layer. The
-printed value for the layer is Total-quantity / Total-count.
-In other words it is an average over the entire Nfreq timescale.
+The {norm} keyword affects how time-averaging is done within for the
+output produced every {Nfreq} timesteps. For an {all} setting, a
+layer quantity is summed over all atoms in all {Nrepeat} samples, as
+is the count of atoms in the layer. The printed value for the layer
+is Total-quantity / Total-count. In other words it is an average over
+the entire {Nfreq} timescale.
For a {sample} setting, the quantity is summed over atoms for only a
single sample, as is the count, and a "average sample value" is
computed, i.e. Sample-quantity / Sample-count. The printed value for
-the layer is the average of the M "average sample values", where M =
-Nfreq/Nevery. In other words it is an average of an average.
-
-If file output is specified, each time info is written to the file, it
-is in the following format. A line with the timestep and number of
-layers is written. Then one line per layer is written, containing the
-layer ID (1-N), the coordinate of the center of the layer, the number
-of atoms in the layer, and one or more calculated values. The number
-of atoms and the value(s) are average quantities. If the value of the
-{units} keyword is {box} or {lattice}, the "coord" is printed in box
-units. If the value of the {units} keyword is {reduced}, the "coord"
-is printed in reduced units (0-1).
-
-If the {density} keyword is used, or the {compute} or {fix} keyword
-with a compute/fix that calculates a single quantity per atom, then a
-single value will be printed for each layer. If the {compute} or
-{fix} keyword is used with a compute/fix that calculates N quantities
-per atom, then N values per line will be written, each of them
-averaged independently.
-
-For the {compute} and {fix} keywords, the calculation performed by the
-compute or fix is on the group defined by the that command. However,
-only atoms in the fix group are included in the layer averaging.
-
-Note that some computes perform costly calculations, involving use of
-or creation of neighbor lists. If the compute is invoked too often by
-fix ave/spatial, it can slow down a simulation.
+the layer is the average of the {Nrepeat} "average sample values", In
+other words it is an average of an average.
+
+The {file} keyword allows a filename to be specified. Every {Nfreq}
+timesteps, layer info will be written to a text file in the following
+format. A line with the timestep and number of layers is written.
+Then one line per layer is written, containing the layer ID (1-N), the
+coordinate of the center of the layer, the number of atoms in the
+layer, and one or more calculated values. The number of atoms and the
+value(s) are average quantities. If the value of the {units} keyword
+is {box} or {lattice}, the "coord" is printed in box units. If the
+value of the {units} keyword is {reduced}, the "coord" is printed in
+reduced units (0-1).
+
+If the style is {density}, or the style is {compute} or {fix} with a
+compute/fix that calculates a single quantity per atom, then a single
+value will be printed for each layer. If the style is {compute} or
+{fix} with a compute/fix that calculates N quantities per atom, then N
+values per line will be written, each of them averaged independently.
+
+The {ave} keyword determines how the layer values produced every
+{Nfreq} steps are averaged with layer values produced on previous
+steps that were multiples of {Nfreq}, before they are accessed by
+another output command or written to a file.
+
+If the {ave} setting is {one}, then the layuer 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 layer values produced on
+timesteps that are multiples of {Nfreq} are summed and averaged in a
+cummulative sense before being output. Each output layer value is
+thus the average of the layer value produced on that timestep with all
+preceeding values for the same layer. 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 layer 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 for the same
+layer 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
+layer 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:]
@@ -208,4 +252,5 @@ minimization"_minimize.html.
[Default:]
-The option defaults are norm = all and units = lattice.
+The option defaults are units = lattice, norm = all, no file output,
+and ave = one.
diff --git a/doc/fix_ave_time.html b/doc/fix_ave_time.html
index b8c560827ea145053738cc76cdd10ce0c928f149..d91ed43122160b5f35ffe976244f52bf8bb623b3 100644
--- a/doc/fix_ave_time.html
+++ b/doc/fix_ave_time.html
@@ -37,8 +37,6 @@
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
@@ -102,7 +100,7 @@ timestep 200, etc.
</P>
<HR>
-<P>Additional optional keywords also affect the averaging.
+<P>Additional optional keywords also affect the operation of this fix.
</P>
<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
@@ -117,8 +115,9 @@ 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.
+produced every <I>Nfreq</I> steps are averaged with values produced on
+previous steps that were multiples of <I>Nfreq</I>, 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
@@ -127,10 +126,10 @@ output as-is without further averaging.
<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.
+average of the value produced 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
@@ -176,6 +175,6 @@ ave/spatial</A>
</P>
<P><B>Default:</B> none
</P>
-<P>The option defaults are style = scalar, no file output, and ave = one.
+<P>The option defaults are type = scalar, no file output, and ave = one.
</P>
</HTML>
diff --git a/doc/fix_ave_time.txt b/doc/fix_ave_time.txt
index 08dec5bc9d6896ed07f18c86c99869162e193dde..61dd38a934a4b559242fab25bcf00edf9d8798b2 100644
--- a/doc/fix_ave_time.txt
+++ b/doc/fix_ave_time.txt
@@ -26,8 +26,6 @@ keyword = {type} or {file} or {ave} :l
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
@@ -90,7 +88,7 @@ timestep 200, etc.
:line
-Additional optional keywords also affect the averaging.
+Additional optional keywords also affect the operation of this fix.
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
@@ -105,8 +103,9 @@ 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.
+produced every {Nfreq} steps are averaged with values produced on
+previous steps that were multiples of {Nfreq}, 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
@@ -115,10 +114,10 @@ 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.
+average of the value produced 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
@@ -164,4 +163,4 @@ ave/spatial"_fix_ave_spatial.html
[Default:] none
-The option defaults are style = scalar, no file output, and ave = one.
+The option defaults are type = scalar, no file output, and ave = one.