2007-02-21 08:18:41 +08:00
|
|
|
<HTML>
|
|
|
|
|
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
|
|
|
|
</CENTER>
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
<HR>
|
|
|
|
|
|
|
|
|
|
<H3>fix ave/spatial command
|
|
|
|
|
</H3>
|
|
|
|
|
<P><B>Syntax:</B>
|
|
|
|
|
</P>
|
2007-10-19 08:33:05 +08:00
|
|
|
<PRE>fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta style arg keyword args ...
|
2007-02-21 08:18:41 +08:00
|
|
|
</PRE>
|
2007-02-21 08:49:36 +08:00
|
|
|
<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
|
|
|
|
|
|
|
|
|
|
<LI>ave/spatial = style name of this fix command
|
|
|
|
|
|
|
|
|
|
<LI>Nevery = calculate property every this many timesteps
|
|
|
|
|
|
2007-09-28 07:25:52 +08:00
|
|
|
<LI>Nrepeat = # of times to repeat the Nevery calculation before averaging
|
|
|
|
|
|
2007-10-15 23:07:59 +08:00
|
|
|
<LI>Nfreq = timestep frequency at which the average value is computed
|
2007-02-21 08:49:36 +08:00
|
|
|
|
|
|
|
|
<LI>dim = <I>x</I> or <I>y</I> or <I>z</I>
|
|
|
|
|
|
|
|
|
|
<LI>origin = <I>lower</I> or <I>center</I> or <I>upper</I> or coordinate value (distance units)
|
|
|
|
|
|
|
|
|
|
<LI>delta = thickness of spatial layers in dim (distance units)
|
|
|
|
|
|
2007-09-28 07:25:52 +08:00
|
|
|
<LI>style = <I>density</I> or <I>compute</I> or <I>fix</I>
|
2007-02-21 08:49:36 +08:00
|
|
|
|
|
|
|
|
<PRE> <I>density</I> arg = <I>mass</I> or <I>number</I>
|
2007-10-19 06:31:18 +08:00
|
|
|
<I>mass</I> = calculate mass density
|
|
|
|
|
<I>number</I> = calculate number density
|
2007-09-28 07:25:52 +08:00
|
|
|
<I>compute</I> arg = compute-ID that stores or calculates per-atom quantities
|
|
|
|
|
<I>fix</I> arg = fix-ID that stores or calculates per-atom quantities
|
|
|
|
|
</PRE>
|
2007-10-19 08:33:05 +08:00
|
|
|
<LI>zero or more keyword/arg pairs may be appended
|
2007-02-21 08:49:36 +08:00
|
|
|
|
2007-10-19 06:27:53 +08:00
|
|
|
<LI>keyword = <I>norm</I> or <I>units</I> or <I>file</I> or <I>ave</I>
|
|
|
|
|
|
2007-10-19 08:33:05 +08:00
|
|
|
<PRE> <I>units</I> arg = <I>box</I> or <I>lattice</I> or <I>reduced</I>
|
|
|
|
|
<I>norm</I> arg = <I>all</I> or <I>sample</I>
|
2007-10-19 06:27:53 +08:00
|
|
|
<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
|
2007-02-21 08:49:36 +08:00
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
2007-02-21 08:18:41 +08:00
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
2007-10-19 06:27:53 +08:00
|
|
|
<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
|
2007-02-21 08:18:41 +08:00
|
|
|
</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
|
2007-10-19 06:27:53 +08:00
|
|
|
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.
|
2007-10-15 23:07:59 +08:00
|
|
|
</P>
|
|
|
|
|
<P>This fix can be used to spatially average per-atom properties
|
|
|
|
|
(velocity, force) or per-atom quantities calculated by a
|
|
|
|
|
<A HREF = "compute.html">compute</A> (energy, stress) or by another fix (see the
|
|
|
|
|
<A HREF = "fix_ave_atom.html">fix ave/atom</A> command) or by a variable via an
|
|
|
|
|
equation you define (see the <A HREF = "compute_variable_atom.html">compute
|
2007-09-28 07:25:52 +08:00
|
|
|
variable/atom</A> command).
|
2007-02-21 08:18:41 +08:00
|
|
|
</P>
|
2007-10-19 06:27:53 +08:00
|
|
|
<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.
|
2007-09-28 07:25:52 +08:00
|
|
|
</P>
|
2007-10-19 06:27:53 +08:00
|
|
|
<P>For style <I>compute</I>, the fix ave/spatial command accesses the
|
2007-09-28 07:25:52 +08:00
|
|
|
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>
|
|
|
|
|
command if you wish to time-average a global quantity calculated by a
|
|
|
|
|
compute without the word atom in its style name, e.g. a compute that
|
|
|
|
|
calculates a temperature or pressure.
|
|
|
|
|
</P>
|
|
|
|
|
<P>See the <A HREF = "compute.html">compute</A> command for a list of pre-defined
|
2007-10-19 06:31:18 +08:00
|
|
|
per-atom computes. Two special computes of note are as follows. The
|
|
|
|
|
<A HREF = "compute_attribute_atom.html">compute attribute/atom</A> command selects
|
|
|
|
|
one or more atom attributes like vx or fz. The "compute
|
|
|
|
|
variable/atom" style can calculate a value for an atom that can be
|
|
|
|
|
specified by a <A HREF = "variable.html">variable atom</A> equation. Users can also
|
|
|
|
|
write code for their own per-atom compute styles and <A HREF = "Section_modify.html">add them to
|
|
|
|
|
LAMMPS</A>. Note that the <A HREF = "dump.html">dump custom</A>
|
|
|
|
|
command can also be used to directly output quantities calculated by a
|
|
|
|
|
per-atom compute in a per-atom fashion.
|
2007-09-28 07:25:52 +08:00
|
|
|
</P>
|
2007-10-19 06:27:53 +08:00
|
|
|
<P>For style <I>fix</I>, the fix ave/spatial command accesses the per-atom
|
2007-09-28 07:25:52 +08:00
|
|
|
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.
|
2007-02-21 08:18:41 +08:00
|
|
|
</P>
|
2007-10-19 06:27:53 +08:00
|
|
|
<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.
|
2007-02-21 08:18:41 +08:00
|
|
|
</P>
|
2007-06-27 05:53:15 +08:00
|
|
|
<P>For orthogonal simulation boxes, the layers are "slices" aligned with
|
2007-06-27 05:47:46 +08:00
|
|
|
the xyz coordinate axes. For non-orthogonal (triclinic) simulation
|
2007-10-19 06:27:53 +08:00
|
|
|
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
|
2007-06-27 05:47:46 +08:00
|
|
|
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
|
|
|
|
|
"b" cross "c" direction. Layers in y have faces normal to the "a"
|
|
|
|
|
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>
|
2007-10-19 06:27:53 +08:00
|
|
|
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.
|
2007-06-27 05:47:46 +08:00
|
|
|
</P>
|
2007-02-21 08:49:36 +08:00
|
|
|
<P>The <I>units</I> keyword determines the meaning of the distance units used
|
2007-06-27 05:47:46 +08:00
|
|
|
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
|
2007-10-19 06:27:53 +08:00
|
|
|
used. For non-orthogonal (triclinic) simulation boxes, only the
|
2007-06-27 05:47:46 +08:00
|
|
|
<I>reduced</I> option may be used.
|
|
|
|
|
</P>
|
|
|
|
|
<P>A <I>box</I> value selects standard distance units as defined by the
|
|
|
|
|
<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
|
|
|
|
|
A <I>lattice</I> value means the distance units are in lattice spacings.
|
|
|
|
|
The <A HREF = "lattice.html">lattice</A> command must have been previously used to
|
|
|
|
|
define the lattice spacing. A <I>reduced</I> value means normalized
|
|
|
|
|
unitless values between 0 and 1, which represent the lower and upper
|
|
|
|
|
faces of the simulation box respectively. Thus an <I>origin</I> value of
|
|
|
|
|
0.5 means the center of the box in any dimension. A <I>delta</I> value of
|
|
|
|
|
0.1 means 10 layers span the box in any dimension.
|
|
|
|
|
</P>
|
|
|
|
|
<P>Consider a non-orthogonal box, with layers in the x dimension. No
|
|
|
|
|
matter how the box is tilted, an <I>origin</I> of 0.0 means start layers at
|
|
|
|
|
the lower "b" cross "c" plane of the simulation box and an <I>origin</I> of
|
|
|
|
|
1.0 means to start layers at the upper "b" cross "c" face of the box.
|
|
|
|
|
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.
|
2007-02-21 08:49:36 +08:00
|
|
|
</P>
|
2007-10-19 06:27:53 +08:00
|
|
|
<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.
|
2007-02-21 08:49:36 +08:00
|
|
|
</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
|
2007-10-19 06:27:53 +08:00
|
|
|
the layer is the average of the <I>Nrepeat</I> "average sample values", In
|
|
|
|
|
other words it is an average of an average.
|
2007-02-21 08:18:41 +08:00
|
|
|
</P>
|
2007-10-19 06:27:53 +08:00
|
|
|
<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>
|
|
|
|
|
|
2007-10-11 06:28:11 +08:00
|
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
2007-06-26 08:03:39 +08:00
|
|
|
</P>
|
|
|
|
|
<P>No information about this fix is written to <A HREF = "restart.html">binary restart
|
|
|
|
|
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
2007-10-15 23:07:59 +08:00
|
|
|
are relevant to this fix.
|
|
|
|
|
</P>
|
|
|
|
|
<P>This fix computes 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. The vector is of length N =
|
|
|
|
|
nlayers*nvalues where nvalues is the number of per-atom quantities
|
|
|
|
|
produced by the compute or fix that fix ave/spatial accesses. Nvalues
|
|
|
|
|
= 1 if the style is <I>density</I>. If nvalues > 1 and vector value N is
|
|
|
|
|
accessed by another output command, then the average quantity for the
|
|
|
|
|
Ith layer and Jth value in that layer is accessed, where I = N /
|
|
|
|
|
nvalues + 1 and J = N % nvalues + 1.
|
|
|
|
|
</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>.
|
2007-06-26 08:03:39 +08:00
|
|
|
</P>
|
2007-10-19 08:33:05 +08:00
|
|
|
<P><B>Restrictions:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P>When the <I>ave</I> keyword is set to <I>running</I> or <I>window</I> then the number
|
|
|
|
|
of layers must remain the same during the simulation, so that the
|
|
|
|
|
appropriate averaging can be done. This will be the case if the
|
|
|
|
|
simulation box size doesn't change or if the <I>units</I> keyword is set to
|
|
|
|
|
<I>reduced</I>.
|
2007-02-21 08:18:41 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
|
|
|
|
<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>
|
|
|
|
|
</P>
|
2007-02-21 08:49:36 +08:00
|
|
|
<P><B>Default:</B>
|
|
|
|
|
</P>
|
2007-10-19 06:27:53 +08:00
|
|
|
<P>The option defaults are units = lattice, norm = all, no file output,
|
|
|
|
|
and ave = one.
|
2007-02-21 08:18:41 +08:00
|
|
|
</P>
|
|
|
|
|
</HTML>
|
