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>
|
2007-02-21 08:49:36 +08:00
|
|
|
<PRE>fix ID group-ID ave/spatial Nevery Nfreq dim origin delta file style args keyword value ...
|
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
|
|
|
|
|
|
|
|
|
|
<LI>Nfreq = write average property to file every this many steps
|
|
|
|
|
|
|
|
|
|
<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)
|
|
|
|
|
|
|
|
|
|
<LI>file = filename to write results to
|
|
|
|
|
|
|
|
|
|
<LI>style = <I>density</I> or <I>atom</I> or <I>compute</I>
|
|
|
|
|
|
|
|
|
|
<PRE> <I>density</I> arg = <I>mass</I> or <I>number</I>
|
|
|
|
|
<I>mass</I> = compute mass density
|
|
|
|
|
<I>number</I> = compute number density
|
|
|
|
|
<I>atom</I> arg = <I>vx</I> or <I>vy</I> or <I>vz</I> or <I>fx</I> or <I>fy</I> or <I>fz</I>
|
|
|
|
|
<I>compute</I> arg = compute-ID that calculates per-atom quantities
|
2007-02-21 08:18:41 +08:00
|
|
|
</PRE>
|
2007-07-03 04:04:44 +08:00
|
|
|
<LI>zero or more keyword/value pairs may be appended
|
2007-02-21 08:49:36 +08:00
|
|
|
|
|
|
|
|
<PRE>keyword = <I>norm</I> or <I>units</I>
|
|
|
|
|
<I>norm</I> value = <I>all</I> or <I>sample</I>
|
2007-06-27 05:47:46 +08:00
|
|
|
<I>units</I> value = <I>box</I> or <I>lattice</I> or <I>reduced</I>
|
2007-02-21 08:49:36 +08:00
|
|
|
</PRE>
|
|
|
|
|
|
|
|
|
|
</UL>
|
2007-02-21 08:18:41 +08:00
|
|
|
<P><B>Examples:</B>
|
|
|
|
|
</P>
|
2007-02-28 06:00:03 +08:00
|
|
|
<PRE>fix 1 all ave/spatial 10000 10000 z lower 2.0 centro.profile compute myCentro
|
|
|
|
|
fix 1 flow ave/spatial 100 1000 y 0.0 1.0 vel.profile atom vx norm sample
|
2007-06-27 05:47:46 +08:00
|
|
|
fix 1 flow ave/spatial 100 1000 y 0.0 2.5 dens.profile density mass
|
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
|
|
|
|
|
longer timescale, and print the results to a file. This can be used
|
|
|
|
|
to spatially average per-atom properties such as velocity or energy or
|
|
|
|
|
a quantity calculated by an equation you define; see the <A HREF = "variable.html">variable
|
|
|
|
|
atom</A> command.
|
|
|
|
|
</P>
|
2007-02-21 08:49:36 +08:00
|
|
|
<P>The <I>density</I> styles means to simply count the number of atoms in each
|
|
|
|
|
layer, either by mass or number. The <I>atom</I> style allows an atom
|
|
|
|
|
property such as x-velocity to be specified. 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. Note that the "compute variable/atom"
|
|
|
|
|
style allows you to calculate any quantity 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 compute styles and <A HREF = "Section_modify.html">add them to
|
2007-02-21 08:18:41 +08:00
|
|
|
LAMMPS</A>. Note that the <A HREF = "dump.html">dump custom</A>
|
|
|
|
|
command can also be used to output per-atom quantities calculated by a
|
|
|
|
|
compute.
|
|
|
|
|
</P>
|
2007-02-21 08:49:36 +08:00
|
|
|
<P>For the <I>compute</I> style, the fix ave/spatial style uses the per-atom
|
2007-02-21 08:18:41 +08:00
|
|
|
scalar or vector calculated by the compute. See the <A HREF = "fix_ave_time.html">fix
|
|
|
|
|
ave/time</A> command if you wish to time-average a
|
|
|
|
|
global quantity, e.g. via a compute that temperature or pressure.
|
|
|
|
|
</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>
|
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
|
2007-06-27 05:53:15 +08:00
|
|
|
boxes, the layers are "tilted slices" that align with the tilted faces
|
2007-06-27 05:47:46 +08:00
|
|
|
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
|
|
|
|
|
"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>
|
|
|
|
|
option must be set to <I>reduced</I>.
|
|
|
|
|
</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
|
|
|
|
|
used. For non-orthongal (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
|
|
|
|
|
<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>
|
2007-02-21 08:18:41 +08:00
|
|
|
<P>The <I>Nevery</I> and <I>Nfreq</I> arguments specify how the property calculated
|
|
|
|
|
for each layer is time-averaged. The property is calculated once each
|
|
|
|
|
Nevery timesteps. It is averaged and output every Nfreq timesteps.
|
|
|
|
|
Nfreq must be a multiple of Nevery. In the 2nd example above, the
|
|
|
|
|
property is calculated every 100 steps. After 10 calculations, the
|
|
|
|
|
average result is written to the file, once every 1000 steps.
|
|
|
|
|
</P>
|
2007-02-21 08:49:36 +08:00
|
|
|
<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>
|
|
|
|
|
<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>
|
2007-02-21 08:18:41 +08:00
|
|
|
<P>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
|
2007-06-27 05:53:15 +08:00
|
|
|
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).
|
2007-02-21 08:18:41 +08:00
|
|
|
</P>
|
|
|
|
|
<P>If the <I>density</I> or <I>atom</I> keyword is used, or the <I>compute</I> keyword
|
|
|
|
|
with a compute that calculates a single quantity per atom, then a
|
|
|
|
|
single value will be printed for each layer. If the <I>compute</I> keyword
|
|
|
|
|
is used with a compute 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> keyword, the calculation performed by the compute in
|
|
|
|
|
on the group defined by the compute. However, only atoms in the fix
|
|
|
|
|
group are included in the layer averaging. LAMMPS prints a warning if
|
|
|
|
|
the fix group and compute group do not match.
|
|
|
|
|
</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.
|
|
|
|
|
</P>
|
2007-06-26 08:03:39 +08:00
|
|
|
<P><B>Restart, fix_modify, thermo output, run start/stop, minimize info:</B>
|
|
|
|
|
</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
|
|
|
|
|
are relevant to this fix. No quantities calculated by this fix can be
|
|
|
|
|
output by the <A HREF = "thermo_style.html">thermo_style custom</A> command. 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>
|
2007-02-21 08:18:41 +08:00
|
|
|
<P><B>Restrictions:</B> none
|
|
|
|
|
</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>
|
|
|
|
|
<P>The option defaults are norm = all and units = lattice.
|
2007-02-21 08:18:41 +08:00
|
|
|
</P>
|
|
|
|
|
</HTML>
|
