git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12721 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -420,11 +420,11 @@ g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
|
||||
package</A>.
|
||||
</P>
|
||||
<DIV ALIGN=center><TABLE BORDER=1 >
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_adapt_fep.html">adapt/fep</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD><TD ><A HREF = "fix_meso.html">meso</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD><TD ><A HREF = "fix_smd.html">smd</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_adapt_fep.html">adapt/fep</A></TD><TD ><A HREF = "fix_addtorque.html">addtorque</A></TD><TD ><A HREF = "fix_atc.html">atc</A></TD><TD ><A HREF = "fix_ave_spatial_sphere.html">ave/spatial/sphere</A></TD><TD ><A HREF = "fix_colvars.html">colvars</A></TD><TD ><A HREF = "fix_imd.html">imd</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_langevin_eff.html">langevin/eff</A></TD><TD ><A HREF = "fix_lb_fluid.html">lb/fluid</A></TD><TD ><A HREF = "fix_lb_momentum.html">lb/momentum</A></TD><TD ><A HREF = "fix_lb_pc.html">lb/pc</A></TD><TD ><A HREF = "fix_lb_rigid_pc_sphere.html">lb/rigid/pc/sphere</A></TD><TD ><A HREF = "fix_lb_viscous.html">lb/viscous</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_meso.html">meso</A></TD><TD ><A HREF = "fix_meso_stationary.html">meso/stationary</A></TD><TD ><A HREF = "fix_nh_eff.html">nph/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">npt/eff</A></TD><TD ><A HREF = "fix_nve_eff.html">nve/eff</A></TD><TD ><A HREF = "fix_nh_eff.html">nvt/eff</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_nvt_sllod_eff.html">nvt/sllod/eff</A></TD><TD ><A HREF = "fix_phonon.html">phonon</A></TD><TD ><A HREF = "fix_qeq_reax.html">qeq/reax</A></TD><TD ><A HREF = "fix_qmmm.html">qmmm</A></TD><TD ><A HREF = "fix_reax_bonds.html">reax/c/bonds</A></TD><TD ><A HREF = "fix_reaxc_species.html">reax/c/species</A></TD></TR>
|
||||
<TR ALIGN="center"><TD ><A HREF = "fix_smd.html">smd</A></TD><TD ><A HREF = "fix_temp_rescale_eff.html">temp/rescale/eff</A></TD><TD ><A HREF = "fix_ti_rs.html">ti/rs</A></TD><TD ><A HREF = "fix_ti_spring.html">ti/spring</A>
|
||||
</TD></TR></TABLE></DIV>
|
||||
|
||||
<HR>
|
||||
|
||||
@ -581,6 +581,7 @@ package"_Section_start.html#start_3.
|
||||
"adapt/fep"_fix_adapt_fep.html,
|
||||
"addtorque"_fix_addtorque.html,
|
||||
"atc"_fix_atc.html,
|
||||
"ave/spatial/sphere"_fix_ave_spatial_sphere.html,
|
||||
"colvars"_fix_colvars.html,
|
||||
"imd"_fix_imd.html,
|
||||
"langevin/eff"_fix_langevin_eff.html,
|
||||
|
||||
@ -81,6 +81,7 @@
|
||||
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 z lower 1.0 y 0.0 2.5 density/mass ave running
|
||||
fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass bound y 5.0 20.0 discard yes ave running
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
@ -405,6 +406,7 @@ simulation box size doesn't change or if the <I>units</I> keyword is set to
|
||||
<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_sphere.html">fix ave/spatial/sphere</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
|
||||
@ -65,7 +65,8 @@ keyword = {region} or {discard} or {norm} or {ave} or {units} or {file} or {over
|
||||
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 z lower 1.0 y 0.0 2.5 density/mass ave running :pre
|
||||
fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass ave running
|
||||
fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass bound y 5.0 20.0 discard yes ave running :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
@ -390,6 +391,7 @@ simulation box size doesn't change or if the {units} keyword is set to
|
||||
"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
|
||||
ave/histo"_fix_ave_histo.html, "fix ave/time"_fix_ave_time.html,
|
||||
"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html,
|
||||
"fix ave/spatial/sphere"_fix_ave_spatial_sphere.html
|
||||
|
||||
[Default:]
|
||||
|
||||
|
||||
342
doc/fix_ave_spatial_sphere.html
Normal file
342
doc/fix_ave_spatial_sphere.html
Normal file
@ -0,0 +1,342 @@
|
||||
<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>
|
||||
323
doc/fix_ave_spatial_sphere.txt
Normal file
323
doc/fix_ave_spatial_sphere.txt
Normal file
@ -0,0 +1,323 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix ave/spatial/sphere command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
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
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
ave/spatial = style name of this fix command :l
|
||||
Nevery = use input values every this many timesteps :l
|
||||
Nrepeat = # of times to use input values for calculating averages :l
|
||||
Nfreq = calculate averages every this many timesteps :l
|
||||
origin_x, origin_y, origin_z = center of the sphere. can be the result of variables or computes (see below) :l
|
||||
r_min = radial distance at which binning begins :l
|
||||
r_max = radial distance at which binning ends :l
|
||||
nbins = number of spherical shells to create between r_min and r_max :l
|
||||
one or more input values can be listed :l
|
||||
value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID\[I\], f_ID, f_ID\[I\], v_name :l
|
||||
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
|
||||
|
||||
zero or more keyword/arg pairs may be appended :l
|
||||
keyword = {region} or {norm} or {units} or {ave} or {file} or {overwrite} or {title1} or {title2} or {title3} :l
|
||||
{region} arg = region-ID
|
||||
region-ID = ID of region atoms must be in to contribute to spatial averaging
|
||||
{norm} arg = {all} or {sample}
|
||||
{units} arg = {box} or {lattice} or {reduced}
|
||||
{ave} args = {one} or {running} or {window M}
|
||||
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
|
||||
{file} arg = filename
|
||||
filename = file to write results to
|
||||
{overwrite} arg = none = overwrite output file with only latest output
|
||||
{title1} arg = string
|
||||
string = text to print as 1st line of output file
|
||||
{title2} arg = string
|
||||
string = text to print as 2nd line of output file
|
||||
{title3} arg = string
|
||||
string = text to print as 3rd line of output file :pre
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
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
|
||||
|
||||
[Description:]
|
||||
|
||||
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 "output
|
||||
commands"_Section_howto.html#howto_15 such as "thermo_style
|
||||
custom"_thermo_style.html, and can also be written to a file.
|
||||
|
||||
The group specified with the command means only atoms within the group
|
||||
contribute to bin averages. If the {region} keyword is used, the atom
|
||||
must be in both the group and the specified geometric
|
||||
"region"_region.html in order to contribute to bin averages.
|
||||
|
||||
Each listed value can be an atom attribute (position, velocity, force
|
||||
component), a mass or number density, or the result of a
|
||||
"compute"_compute.html or "fix"_fix.html or the evaluation of an
|
||||
atom-style "variable"_variable.html. 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 "fix
|
||||
ave/time"_fix_ave_time.html command.
|
||||
|
||||
"Computes"_compute.html that produce per-atom quantities are those
|
||||
which have the word {atom} in their style name. See the doc pages for
|
||||
individual "fixes"_fix.html to determine which ones produce per-atom
|
||||
quantities. "Variables"_variable.html of style {atom} are the only
|
||||
ones that can be used with this fix since all other styles of variable
|
||||
produce global quantities.
|
||||
|
||||
The per-atom values of each input vector are binned and averaged
|
||||
independently of the per-atom values in other input vectors.
|
||||
|
||||
{Nbins} specifies the number of spherical shells which will be created
|
||||
between r_min and r_max centered at (origin_x, origin_y, origin_z).
|
||||
|
||||
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.
|
||||
|
||||
:line
|
||||
|
||||
The {Nevery}, {Nrepeat}, and {Nfreq} 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 {Nfreq}. The average is over {Nrepeat}
|
||||
quantities, computed in the preceding 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. Also, the timesteps
|
||||
contributing to the average value cannot overlap, i.e. Nfreq >
|
||||
(Nrepeat-1)*Nevery is required.
|
||||
|
||||
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.
|
||||
|
||||
:line
|
||||
|
||||
The {origin_x}, {origin_y}, and {origin_z} 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.
|
||||
|
||||
:line
|
||||
|
||||
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 "compute
|
||||
property/atom"_compute_property_atom.html command and then specifying
|
||||
an input value from that compute.
|
||||
|
||||
The {density/number} value means the number density is computed in
|
||||
each bin, i.e. a weighting of 1 for each atom. The {density/mass}
|
||||
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 "units"_units.html 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 {units} keyword in this command.
|
||||
|
||||
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 "add them to LAMMPS"_Section_modify.html.
|
||||
|
||||
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
|
||||
{Nevery}, else an error results. Users can also write code for their
|
||||
own fix styles and "add them to LAMMPS"_Section_modify.html.
|
||||
|
||||
If a value begins with "v_", a variable name must follow which has
|
||||
been previously defined in the input script. Variables of style
|
||||
{atom} 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.
|
||||
|
||||
:line
|
||||
|
||||
Additional optional keywords also affect the operation of this fix.
|
||||
The {region} keyword was discussed above.
|
||||
|
||||
The {norm} keyword affects how averaging is done for the output
|
||||
produced every {Nfreq} timesteps. For an {all} setting, a bin
|
||||
quantity is summed over all atoms in all {Nrepeat} 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 {Nfreq} timescale.
|
||||
|
||||
For a {sample} 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 {Nrepeat} "average sample values", In
|
||||
other words it is an average of an average.
|
||||
|
||||
The {ave} keyword determines how the bin values produced every {Nfreq}
|
||||
steps are averaged with bin 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 bin 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 bin values produced on
|
||||
timesteps that are multiples of {Nfreq} 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 "unfix"_unfix.html command, or re-defining the fix by
|
||||
re-specifying it.
|
||||
|
||||
If the {ave} setting is {window}, then the bin 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 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.
|
||||
|
||||
The {units} 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 {reduced} option
|
||||
may be used.
|
||||
|
||||
A {box} value selects standard distance units as defined by the
|
||||
"units"_units.html command, e.g. Angstroms for units = real or metal.
|
||||
A {lattice} value means the distance units are in lattice spacings.
|
||||
The "lattice"_lattice.html command must have been previously used to
|
||||
define the lattice spacing.
|
||||
|
||||
IMPORTANT NOTE: The {lattice} style may only be used if the lattice
|
||||
spacing is the same in each direction.
|
||||
|
||||
A {reduced} value means normalized unitless values between 0 and 1,
|
||||
which represent the lower and upper faces of the simulation box
|
||||
respectively. Thus an {origin} value of 0.5 means the center of the
|
||||
box in any dimension.
|
||||
|
||||
The {file} keyword allows a filename to be specified. Every {Nfreq}
|
||||
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 {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).
|
||||
|
||||
The {overwrite} 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 {ave running} setting.
|
||||
|
||||
The {title1} and {title2} and {title3} keywords allow specification of
|
||||
the strings that will be printed as the first 3 lines of the output
|
||||
file, assuming the {file} keyword was used. LAMMPS uses default
|
||||
values for each of these, so they do not need to be specified.
|
||||
|
||||
By default, these header lines are as follows:
|
||||
|
||||
# Spatial-averaged data for fix ID and group name
|
||||
# Timestep Number-of-bins
|
||||
# Bin r Count value1 value2 ... :pre
|
||||
|
||||
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.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix.
|
||||
|
||||
This fix computes a global array of values which can be accessed by
|
||||
various "output commands"_Section_howto.html#howto_15. The values can
|
||||
only be accessed on timesteps that are multiples of {Nfreq} 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 {reduced}, this is in
|
||||
reduced units, while for units {box} and {lattice} 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.
|
||||
|
||||
No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
When the {ave} keyword is set to {running} or {window} 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 {units} keyword is set to
|
||||
{reduced}.
|
||||
|
||||
This style is part of the USER-MISC package. It is only enabled if
|
||||
LAMMPS is build with that package. See the "Making of
|
||||
LAMMPS"_Section_start.html#3 section for more info.
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"compute"_compute.html, "fix ave/atom"_fix_ave_atom.html, "fix
|
||||
ave/histo"_fix_ave_histo.html, "fix ave/time"_fix_ave_time.html,
|
||||
"variable"_variable.html, "fix ave/correlate"_fix_ave_correlate.html,
|
||||
"fix ave/spatial"_fix_ave_spatial.html,
|
||||
|
||||
[Default:]
|
||||
|
||||
The option defaults are norm = all, ave = one, units = lattice, no
|
||||
file output, and title 1,2,3 = strings as described above.
|
||||
Reference in New Issue
Block a user