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doc/fix_ave_spatial.html
+ 122
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......@@ -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>
doc/fix_ave_spatial.txt
+ 121
− 76
View file @ 721cd167
......@@ -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.
doc/fix_ave_time.html
+ 9
− 10
View file @ 721cd167
......@@ -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>
doc/fix_ave_time.txt
+ 9
− 10
View file @ 721cd167
......@@ -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.
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