forked from lijiext/lammps
332 lines
16 KiB
HTML
332 lines
16 KiB
HTML
<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>
|
|
<PRE>fix ID group-ID ave/spatial Nevery Nrepeat Nfreq dim origin delta value1 value2 ... keyword args ...
|
|
</PRE>
|
|
<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 = use input values every this many timesteps
|
|
|
|
<LI>Nrepeat = # of times to use input values for calculating averages
|
|
|
|
<LI>Nfreq = calculate averages every this many timesteps
|
|
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>one or more input values can be listed
|
|
|
|
<LI>value = x, y, z, vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name
|
|
|
|
<PRE> x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
|
|
density/number, density/mass = number or mass density
|
|
c_ID = per-atom vector calculated by a compute with ID
|
|
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
|
|
f_ID = per-atom vector calculated by a fix with ID
|
|
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
|
|
v_name = per-atom vector calculated by an atom-style variable with name
|
|
</PRE>
|
|
<LI>zero or more keyword/arg pairs may be appended
|
|
|
|
<LI>keyword = <I>norm</I> or <I>units</I> or <I>file</I> or <I>ave</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
|
|
|
|
<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>
|
|
<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 cumulative average of all previous Nfreq steps
|
|
window M = output average of M most recent Nfreq steps
|
|
<I>title1</I> arg = string
|
|
string = text to print as 1st line of output file
|
|
<I>title2</I> arg = string
|
|
string = text to print as 2nd line of output file
|
|
<I>title3</I> arg = string
|
|
string = text to print as 3rd line of output file
|
|
</PRE>
|
|
|
|
</UL>
|
|
<P><B>Examples:</B>
|
|
</P>
|
|
<PRE>fix 1 all ave/spatial 10000 1 10000 z lower 0.02 c_myCentro units reduced &
|
|
title1 "My output values"
|
|
fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz 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>Use one or more per-atom vectors as inputs every few timesteps, bin
|
|
them spatially by layer in a dimension, and average the layer values
|
|
over longer timescales. The resulting layer 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 can also be written to a file.
|
|
</P>
|
|
<P>The group specified with the command means only atoms within the group
|
|
contribute to layer averages.
|
|
</P>
|
|
<P>Each listed value can be an atom attribute (position, velocity, force
|
|
component), a mass or number density, or the result of a
|
|
<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or the evaluation of an
|
|
atom-style <A HREF = "variable.html">variable</A>. In the latter cases, the
|
|
compute, fix, or variable must produce a per-atom quantity, not a
|
|
global quantity. If you wish to time-average global quantities from a
|
|
compute, fix, or variable, then see the <A HREF = "fix_ave_time.html">fix
|
|
ave/time</A> command.
|
|
</P>
|
|
<P><A HREF = "compute.html">Computes</A> that produce per-atom quantities are those
|
|
which have the word <I>atom</I> in their style name. See the doc pages for
|
|
individual <A HREF = "fix.html">fixes</A> to determine which ones produce per-atom
|
|
quantities. <A HREF = "variable.html">Variables</A> of style <I>atom</I> are the only
|
|
ones that can be used with this fix since all other styles of variable
|
|
produce global quantities.
|
|
</P>
|
|
<P>The per-atom values of each input vector are binned and averaged
|
|
independently of the per-atom values in other input vectors.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
|
|
timesteps the input values will be used to bin them into layers and
|
|
contribute to the average. The final averaged quantities are
|
|
generated every <I>Nfreq</I> timesteps. The average is over <I>Nrepeat</I>
|
|
quantities, computed in the preceding 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. Also, the timesteps
|
|
contributing to the average value cannot overlap, i.e. Nfreq >
|
|
(Nrepeat-1)*Nevery is required.
|
|
</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. Similarly for timesteps 190,192,194,196,198,200 on
|
|
timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
|
|
averaging is done; values are simply generated on timesteps
|
|
100,200,etc.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>Each 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
|
|
simulation 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 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
|
|
"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> when using a non-orthogonal simulation
|
|
box, as discussed below.
|
|
</P>
|
|
<HR>
|
|
|
|
<P>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
|
|
self-explanatory. Note that other atom attributes can be used as
|
|
inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
|
|
property/atom</A> command and then specifying
|
|
an input value from that compute.
|
|
</P>
|
|
<P>The <I>density/number</I> value means the number density is computed in
|
|
each layer, i.e. a weighting of 1 for each atom. The <I>density/mass</I>
|
|
value means the mass density is computed in each layer, i.e. each atom
|
|
is weighted by its mass. The resulting density is normalized by the
|
|
volume of the layer so that units of number/volume or mass/volume are
|
|
output.
|
|
</P>
|
|
<P>If a value begins with "c_", a compute ID must follow which has been
|
|
previously defined in the input script. If no bracketed integer is
|
|
appended, the per-atom vector calculated by the compute is used. If a
|
|
bracketed interger is appended, the Ith column of the per-atom array
|
|
calculated by the compute is used. Users can also write code for
|
|
their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
|
|
</P>
|
|
<P>If a value begins with "f_", a fix ID must follow which has been
|
|
previously defined in the input script. If no bracketed integer is
|
|
appended, the per-atom vector calculated by the fix is used. If a
|
|
bracketed integer is appended, the Ith column of the per-atom array
|
|
calculated by the fix is used. Note that some fixes only produce
|
|
their values on certain timesteps, which must be compatible with
|
|
<I>Nevery</I>, else an error results. Users can also write code for their
|
|
own fix styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
|
|
</P>
|
|
<P>If a value begins with "v_", a variable name must follow which has
|
|
been previously defined in the input script. Variables of style
|
|
<I>atom</I> can reference thermodynamic keywords and various per-atom
|
|
attributes, or invoke other computes, fixes, or variables when they
|
|
are evaluated, so this is a very general means of generating per-atom
|
|
quantities to spatially average.
|
|
</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-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
|
|
<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.
|
|
</P>
|
|
<P>The <I>norm</I> keyword affects how averaging is done 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 layer 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 <I>Nrepeat</I> "average sample values", In
|
|
other words it is an average of an average.
|
|
</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 layer 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
|
|
cumulative sense before being output. Each output layer value is
|
|
thus the average of the layer value produced on that timestep with all
|
|
preceding 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>
|
|
<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
|
|
timesteps, a section of 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
|
|
values in each line corresponds to the number of values specified in
|
|
the fix ave/spatial command. 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>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
|
|
the strings that will be printed as the first 3 lines of the output
|
|
file, assuming the <I>file</I> keyword was used. LAMMPS uses default
|
|
values for each of these, so they do not need to be specified.
|
|
</P>
|
|
<P>By default, these header lines are as follows:
|
|
</P>
|
|
<PRE># Spatial-averaged data for fix ID and group name
|
|
# Timestep Number-of-layers
|
|
# Layer Coord Count value1 value2 ...
|
|
</PRE>
|
|
<P>In the first line, ID and name are replaced with the fix-ID and group
|
|
name. The second line describes the two values that are printed at
|
|
the first of each section of output. In the third line the values are
|
|
replaced with the appropriate fields from the fix ave/spatial command.
|
|
</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
|
|
files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
|
|
are relevant to this fix.
|
|
</P>
|
|
<P>This fix computes a global array of values which can be accessed by
|
|
various <A HREF = "Section_howto.html#4_15">output commands</A>. The values can
|
|
only be accessed on timesteps that are multiples of <I>Nfreq</I> since that
|
|
is when averaging is performed. The global array has # of rows =
|
|
Nlayers and # of columns = Nvalues+2. The first column has the layer
|
|
coordinate (center of the layer), the 2nd column has the count of
|
|
atoms in that layer, and the remaining columns are the Nvalue
|
|
quantities. When the array is accessed with an I that exceeds the
|
|
current number of layers, than a 0.0 is returned by the fix instead of
|
|
an error, since the number of layers can vary as a simulation runs,
|
|
depending on the simulation box size. The array values calculated by
|
|
this fix are "intensive", meaning they are independent of the number
|
|
of atoms in the simulation, since they are already normalized by the
|
|
count of atoms in each layer.
|
|
</P>
|
|
<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
|
|
the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
|
|
minimization</A>.
|
|
</P>
|
|
<P><B>Restrictions:</B>
|
|
</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>.
|
|
</P>
|
|
<P><B>Related commands:</B>
|
|
</P>
|
|
<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_histo.html">fix
|
|
ave/histo</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>,
|
|
<A HREF = "variable.html">variable</A>,
|
|
</P>
|
|
<P><B>Default:</B>
|
|
</P>
|
|
<P>The option defaults are units = lattice, norm = all, no file output,
|
|
and ave = one, title 1,2,3 = strings as described above.
|
|
</P>
|
|
</HTML>
|