forked from lijiext/lammps
343 lines
17 KiB
HTML
343 lines
17 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/sphere command
|
||
|
|
</H3>
|
||
|
|
<P><B>Syntax:</B>
|
||
|
|
</P>
|
||
|
|
<PRE>fix ID group-ID ave/spatial/sphere Nevery Nrepeat Nfreq origin_x origin_y origin_z r_min r_max nbins 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
|
||
|
|
|
||
|
|
<LI>origin_x, origin_y, origin_z = center of the sphere. can be the result of variables or computes (see below)
|
||
|
|
|
||
|
|
<LI>r_min = radial distance at which binning begins
|
||
|
|
|
||
|
|
<LI>r_max = radial distance at which binning ends
|
||
|
|
|
||
|
|
<LI>nbins = number of spherical shells to create between r_min and r_max
|
||
|
|
|
||
|
|
<LI>one or more input values can be listed
|
||
|
|
|
||
|
|
<LI>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name
|
||
|
|
|
||
|
|
<PRE> 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>region</I> or <I>norm</I> or <I>units</I> or <I>ave</I> or <I>file</I> or <I>overwrite</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
|
||
|
|
|
||
|
|
<PRE> <I>region</I> arg = region-ID
|
||
|
|
region-ID = ID of region atoms must be in to contribute to spatial averaging
|
||
|
|
<I>norm</I> arg = <I>all</I> or <I>sample</I>
|
||
|
|
<I>units</I> arg = <I>box</I> or <I>lattice</I> or <I>reduced</I>
|
||
|
|
<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>file</I> arg = filename
|
||
|
|
filename = file to write results to
|
||
|
|
<I>overwrite</I> arg = none = overwrite output file with only latest output
|
||
|
|
<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/sphere 10000 1 10000 0.5 0.5 0.5 0.1 0.5 5 density/number vx vy vz units reduced title1 "My output values"
|
||
|
|
fix 1 flow ave/spatial/sphere 100 10 1000 20.0 20.0 20.0 0.0 20.0 20 vx vz norm sample file vel.profile
|
||
|
|
</PRE>
|
||
|
|
<P><B>Description:</B>
|
||
|
|
</P>
|
||
|
|
<P>Use one or more per-atom vectors as inputs every few timesteps, bin
|
||
|
|
their values spatially into spherical shells based on current atom
|
||
|
|
coordinates, and average the bin values over longer timescales. The
|
||
|
|
resulting bin averages can be used by other <A HREF = "Section_howto.html#howto_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 bin averages. If the <I>region</I> keyword is used, the atom
|
||
|
|
must be in both the group and the specified geometric
|
||
|
|
<A HREF = "region.html">region</A> in order to contribute to bin 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>
|
||
|
|
<P><I>Nbins</I> specifies the number of spherical shells which will be created
|
||
|
|
between r_min and r_max centered at (origin_x, origin_y, origin_z).
|
||
|
|
</P>
|
||
|
|
<P>IMPORTANT NOTE: This fix works by creating an array of size Nbins by
|
||
|
|
Nvalues on each processor. Nbins is the total number of bins; Nvalues
|
||
|
|
is the number of input values specified. Each processor loops over
|
||
|
|
its atoms, tallying its values to the appropriate bin. Then the
|
||
|
|
entire array is summed across all processors. This means that using a
|
||
|
|
large number of bins will incur an overhead in memory and computational
|
||
|
|
cost (summing across processors), so be careful to use reasonable numbers
|
||
|
|
of bins.
|
||
|
|
</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 and contribute to
|
||
|
|
the average. The final averaged quantities are generated on timesteps
|
||
|
|
that are a multiples of <I>Nfreq</I>. 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>The <I>origin_x</I>, <I>origin_y</I>, and <I>origin_z</I> parameters may be specified
|
||
|
|
by either a compute or a variable. This allows, for example, the
|
||
|
|
center of the spherical bins to be attached to the center of mass of a
|
||
|
|
group of atoms. If a variable origin is used and periodic boundary
|
||
|
|
conditions are in effect, then the origin will be wrapped across
|
||
|
|
periodic boundaries whenever it changes so that it is always inside
|
||
|
|
the simulation box.
|
||
|
|
</P>
|
||
|
|
<HR>
|
||
|
|
|
||
|
|
<P>The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
|
||
|
|
Note that other atom attributes (including atom postitions x,y,z) 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 bin, i.e. a weighting of 1 for each atom. The <I>density/mass</I>
|
||
|
|
value means the mass density is computed in each bin, i.e. each atom
|
||
|
|
is weighted by its mass. The resulting density is normalized by the
|
||
|
|
volume of the bin so that units of number/volume or density are
|
||
|
|
output. See the <A HREF = "units.html">units</A> command doc page for the
|
||
|
|
definition of density for each choice of units, e.g. gram/cm^3.
|
||
|
|
The bin volume will always be calculated in box units, independent
|
||
|
|
of the use of the <I>units</I> keyword in this command.
|
||
|
|
</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 integer 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.
|
||
|
|
The <I>region</I> keyword was discussed above.
|
||
|
|
</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 bin
|
||
|
|
quantity is summed over all atoms in all <I>Nrepeat</I> samples, as is the
|
||
|
|
count of atoms in the bin. The printed value for the bin 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 bin 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 bin 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 bin values produced every <I>Nfreq</I>
|
||
|
|
steps are averaged with bin 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 bin 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 bin values produced on
|
||
|
|
timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
|
||
|
|
cumulative sense before being output. Each output bin value is thus
|
||
|
|
the average of the bin value produced on that timestep with all
|
||
|
|
preceding values for the same bin. 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 bin 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 bin
|
||
|
|
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 bin
|
||
|
|
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>units</I> keyword determines the meaning of the distance units used
|
||
|
|
for the sphere origin and the two radial lengths. 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.
|
||
|
|
</P>
|
||
|
|
<P>IMPORTANT NOTE: The <I>lattice</I> style may only be used if the lattice
|
||
|
|
spacing is the same in each direction.
|
||
|
|
</P>
|
||
|
|
<P>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.
|
||
|
|
</P>
|
||
|
|
<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
|
||
|
|
timesteps, a section of bin info will be written to a text file in the
|
||
|
|
following format. A line with the timestep and number of bin is
|
||
|
|
written. Then one line per bin is written, containing the bin ID
|
||
|
|
(1-N), the coordinate of the center of the bin, the number of atoms in
|
||
|
|
the bin, 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>overwrite</I> keyword will continuously overwrite the output file
|
||
|
|
with the latest output, so that it only contains one timestep worth of
|
||
|
|
output. This option can only be used with the <I>ave running</I> setting.
|
||
|
|
</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-bins
|
||
|
|
# Bin r 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.
|
||
|
|
The Coord2 and Coord3 entries in the third line only appear for 2d and
|
||
|
|
3d bins respectively. For 1d bins, the word Coord1 is replaced by
|
||
|
|
just Coord.
|
||
|
|
</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#howto_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 =
|
||
|
|
Nbins and # of columns = 2+Nvalues. The first column contains the
|
||
|
|
radius at the center of the shell. For units <I>reduced</I>, this is in
|
||
|
|
reduced units, while for units <I>box</I> and <I>lattice</I> this is in box
|
||
|
|
units. The next column has the count of atoms in that bin, and the
|
||
|
|
remaining columns are the Nvalue quantities. When the array is
|
||
|
|
accessed with an I that exceeds the current number of bins, than a 0.0
|
||
|
|
is returned by the fix instead of an error. The array values
|
||
|
|
calculated by this fix are "intensive", since they are already
|
||
|
|
normalized by the count of atoms in each bin.
|
||
|
|
</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 bins 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>This style is part of the USER-MISC package. It is only enabled if
|
||
|
|
LAMMPS is build with that package. See the <A HREF = "Section_start.html#3">Making of
|
||
|
|
LAMMPS</A> section for more info.
|
||
|
|
</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>, <A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
|
||
|
|
<A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
|
||
|
|
</P>
|
||
|
|
<P><B>Default:</B>
|
||
|
|
</P>
|
||
|
|
<P>The option defaults are norm = all, ave = one, units = lattice, no
|
||
|
|
file output, and title 1,2,3 = strings as described above.
|
||
|
|
</P>
|
||
|
|
</HTML>
|