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343 lines
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<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>
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<H3>fix ave/spatial/sphere command
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</H3>
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<P><B>Syntax:</B>
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</P>
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<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 ...
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</PRE>
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<UL><LI>ID, group-ID are documented in <A HREF = "fix.html">fix</A> command
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<LI>ave/spatial = style name of this fix command
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<LI>Nevery = use input values every this many timesteps
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<LI>Nrepeat = # of times to use input values for calculating averages
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<LI>Nfreq = calculate averages every this many timesteps
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<LI>origin_x, origin_y, origin_z = center of the sphere. can be the result of variables or computes (see below)
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<LI>r_min = radial distance at which binning begins
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<LI>r_max = radial distance at which binning ends
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<LI>nbins = number of spherical shells to create between r_min and r_max
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<LI>one or more input values can be listed
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<LI>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, c_ID, c_ID[I], f_ID, f_ID[I], v_name
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<PRE> vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
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density/number, density/mass = number or mass density
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c_ID = per-atom vector calculated by a compute with ID
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c_ID[I] = Ith column of per-atom array calculated by a compute with ID
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f_ID = per-atom vector calculated by a fix with ID
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f_ID[I] = Ith column of per-atom array calculated by a fix with ID
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v_name = per-atom vector calculated by an atom-style variable with name
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</PRE>
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<LI>zero or more keyword/arg pairs may be appended
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<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>
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<PRE> <I>region</I> arg = region-ID
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region-ID = ID of region atoms must be in to contribute to spatial averaging
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<I>norm</I> arg = <I>all</I> or <I>sample</I>
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<I>units</I> arg = <I>box</I> or <I>lattice</I> or <I>reduced</I>
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<I>ave</I> args = <I>one</I> or <I>running</I> or <I>window M</I>
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one = output new average value every Nfreq steps
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running = output cumulative average of all previous Nfreq steps
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window M = output average of M most recent Nfreq steps
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<I>file</I> arg = filename
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filename = file to write results to
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<I>overwrite</I> arg = none = overwrite output file with only latest output
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<I>title1</I> arg = string
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string = text to print as 1st line of output file
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<I>title2</I> arg = string
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string = text to print as 2nd line of output file
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<I>title3</I> arg = string
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string = text to print as 3rd line of output file
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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<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"
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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
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</PRE>
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<P><B>Description:</B>
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</P>
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<P>Use one or more per-atom vectors as inputs every few timesteps, bin
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their values spatially into spherical shells based on current atom
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coordinates, and average the bin values over longer timescales. The
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resulting bin averages can be used by other <A HREF = "Section_howto.html#howto_15">output
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commands</A> such as <A HREF = "thermo_style.html">thermo_style
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custom</A>, and can also be written to a file.
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</P>
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<P>The group specified with the command means only atoms within the group
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contribute to bin averages. If the <I>region</I> keyword is used, the atom
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must be in both the group and the specified geometric
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<A HREF = "region.html">region</A> in order to contribute to bin averages.
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</P>
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<P>Each listed value can be an atom attribute (position, velocity, force
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component), a mass or number density, or the result of a
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<A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or the evaluation of an
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atom-style <A HREF = "variable.html">variable</A>. In the latter cases, the
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compute, fix, or variable must produce a per-atom quantity, not a
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global quantity. If you wish to time-average global quantities from a
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compute, fix, or variable, then see the <A HREF = "fix_ave_time.html">fix
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ave/time</A> command.
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</P>
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<P><A HREF = "compute.html">Computes</A> that produce per-atom quantities are those
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which have the word <I>atom</I> in their style name. See the doc pages for
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individual <A HREF = "fix.html">fixes</A> to determine which ones produce per-atom
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quantities. <A HREF = "variable.html">Variables</A> of style <I>atom</I> are the only
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ones that can be used with this fix since all other styles of variable
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produce global quantities.
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</P>
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<P>The per-atom values of each input vector are binned and averaged
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independently of the per-atom values in other input vectors.
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</P>
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<P><I>Nbins</I> specifies the number of spherical shells which will be created
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between r_min and r_max centered at (origin_x, origin_y, origin_z).
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</P>
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<P>IMPORTANT NOTE: This fix works by creating an array of size Nbins by
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Nvalues on each processor. Nbins is the total number of bins; Nvalues
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is the number of input values specified. Each processor loops over
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its atoms, tallying its values to the appropriate bin. Then the
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entire array is summed across all processors. This means that using a
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large number of bins will incur an overhead in memory and computational
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cost (summing across processors), so be careful to use reasonable numbers
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of bins.
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</P>
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<HR>
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<P>The <I>Nevery</I>, <I>Nrepeat</I>, and <I>Nfreq</I> arguments specify on what
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timesteps the input values will be used to bin them and contribute to
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the average. The final averaged quantities are generated on timesteps
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that are a multiples of <I>Nfreq</I>. The average is over <I>Nrepeat</I>
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quantities, computed in the preceding portion of the simulation every
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<I>Nevery</I> timesteps. <I>Nfreq</I> must be a multiple of <I>Nevery</I> and
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<I>Nevery</I> must be non-zero even if <I>Nrepeat</I> is 1. Also, the timesteps
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contributing to the average value cannot overlap, i.e. Nfreq >
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(Nrepeat-1)*Nevery is required.
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</P>
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<P>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then values on
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timesteps 90,92,94,96,98,100 will be used to compute the final average
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on timestep 100. Similarly for timesteps 190,192,194,196,198,200 on
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timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
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averaging is done; values are simply generated on timesteps
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100,200,etc.
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</P>
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<HR>
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<P>The <I>origin_x</I>, <I>origin_y</I>, and <I>origin_z</I> parameters may be specified
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by either a compute or a variable. This allows, for example, the
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center of the spherical bins to be attached to the center of mass of a
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group of atoms. If a variable origin is used and periodic boundary
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conditions are in effect, then the origin will be wrapped across
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periodic boundaries whenever it changes so that it is always inside
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the simulation box.
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</P>
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<HR>
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<P>The atom attribute values (vx,vy,vz,fx,fy,fz) are self-explanatory.
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Note that other atom attributes (including atom postitions x,y,z) can
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be used as inputs to this fix by using the <A HREF = "compute_property_atom.html">compute
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property/atom</A> command and then specifying
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an input value from that compute.
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</P>
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<P>The <I>density/number</I> value means the number density is computed in
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each bin, i.e. a weighting of 1 for each atom. The <I>density/mass</I>
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value means the mass density is computed in each bin, i.e. each atom
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is weighted by its mass. The resulting density is normalized by the
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volume of the bin so that units of number/volume or density are
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output. See the <A HREF = "units.html">units</A> command doc page for the
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definition of density for each choice of units, e.g. gram/cm^3.
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The bin volume will always be calculated in box units, independent
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of the use of the <I>units</I> keyword in this command.
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</P>
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<P>If a value begins with "c_", a compute ID must follow which has been
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previously defined in the input script. If no bracketed integer is
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appended, the per-atom vector calculated by the compute is used. If a
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bracketed integer is appended, the Ith column of the per-atom array
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calculated by the compute is used. Users can also write code for
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their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
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</P>
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<P>If a value begins with "f_", a fix ID must follow which has been
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previously defined in the input script. If no bracketed integer is
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appended, the per-atom vector calculated by the fix is used. If a
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bracketed integer is appended, the Ith column of the per-atom array
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calculated by the fix is used. Note that some fixes only produce
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their values on certain timesteps, which must be compatible with
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<I>Nevery</I>, else an error results. Users can also write code for their
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own fix styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>.
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</P>
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<P>If a value begins with "v_", a variable name must follow which has
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been previously defined in the input script. Variables of style
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<I>atom</I> can reference thermodynamic keywords and various per-atom
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attributes, or invoke other computes, fixes, or variables when they
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are evaluated, so this is a very general means of generating per-atom
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quantities to spatially average.
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</P>
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<HR>
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<P>Additional optional keywords also affect the operation of this fix.
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The <I>region</I> keyword was discussed above.
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</P>
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<P>The <I>norm</I> keyword affects how averaging is done for the output
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produced every <I>Nfreq</I> timesteps. For an <I>all</I> setting, a bin
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quantity is summed over all atoms in all <I>Nrepeat</I> samples, as is the
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count of atoms in the bin. The printed value for the bin is
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Total-quantity / Total-count. In other words it is an average over
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the entire <I>Nfreq</I> timescale.
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</P>
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<P>For a <I>sample</I> setting, the bin quantity is summed over atoms for only
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a single sample, as is the count, and a "average sample value" is
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computed, i.e. Sample-quantity / Sample-count. The printed value for
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the bin is the average of the <I>Nrepeat</I> "average sample values", In
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other words it is an average of an average.
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</P>
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<P>The <I>ave</I> keyword determines how the bin values produced every <I>Nfreq</I>
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steps are averaged with bin values produced on previous steps that
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were multiples of <I>Nfreq</I>, before they are accessed by another output
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command or written to a file.
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</P>
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<P>If the <I>ave</I> setting is <I>one</I>, then the bin values produced on
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timesteps that are multiples of <I>Nfreq</I> are independent of each other;
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they are output as-is without further averaging.
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</P>
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<P>If the <I>ave</I> setting is <I>running</I>, then the bin values produced on
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timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
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cumulative sense before being output. Each output bin value is thus
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the average of the bin value produced on that timestep with all
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preceding values for the same bin. This running average begins when
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the fix is defined; it can only be restarted by deleting the fix via
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the <A HREF = "unfix.html">unfix</A> command, or re-defining the fix by
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re-specifying it.
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</P>
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<P>If the <I>ave</I> setting is <I>window</I>, then the bin values produced on
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timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
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a moving "window" of time, so that the last M values for the same bin
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are used to produce the output. E.g. if M = 3 and Nfreq = 1000, then
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the output on step 10000 will be the average of the individual bin
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values on steps 8000,9000,10000. Outputs on early steps will average
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over less than M values if they are not available.
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</P>
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<P>The <I>units</I> keyword determines the meaning of the distance units used
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for the sphere origin and the two radial lengths. For orthogonal
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simulation boxes, any of the 3 options may be used. For
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non-orthogonal (triclinic) simulation boxes, only the <I>reduced</I> option
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may be used.
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</P>
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<P>A <I>box</I> value selects standard distance units as defined by the
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<A HREF = "units.html">units</A> command, e.g. Angstroms for units = real or metal.
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A <I>lattice</I> value means the distance units are in lattice spacings.
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The <A HREF = "lattice.html">lattice</A> command must have been previously used to
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define the lattice spacing.
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</P>
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<P>IMPORTANT NOTE: The <I>lattice</I> style may only be used if the lattice
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spacing is the same in each direction.
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</P>
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<P>A <I>reduced</I> value means normalized unitless values between 0 and 1,
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which represent the lower and upper faces of the simulation box
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respectively. Thus an <I>origin</I> value of 0.5 means the center of the
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box in any dimension.
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</P>
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<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
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timesteps, a section of bin info will be written to a text file in the
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following format. A line with the timestep and number of bin is
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written. Then one line per bin is written, containing the bin ID
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(1-N), the coordinate of the center of the bin, the number of atoms in
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the bin, and one or more calculated values. The number of values in
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each line corresponds to the number of values specified in the fix
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ave/spatial command. The number of atoms and the value(s) are average
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quantities. If the value of the <I>units</I> keyword is <I>box</I> or
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<I>lattice</I>, the "coord" is printed in box units. If the value of the
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<I>units</I> keyword is <I>reduced</I>, the "coord" is printed in reduced units
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(0-1).
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</P>
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<P>The <I>overwrite</I> keyword will continuously overwrite the output file
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with the latest output, so that it only contains one timestep worth of
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output. This option can only be used with the <I>ave running</I> setting.
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</P>
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<P>The <I>title1</I> and <I>title2</I> and <I>title3</I> keywords allow specification of
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the strings that will be printed as the first 3 lines of the output
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file, assuming the <I>file</I> keyword was used. LAMMPS uses default
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values for each of these, so they do not need to be specified.
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</P>
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<P>By default, these header lines are as follows:
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</P>
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<PRE># Spatial-averaged data for fix ID and group name
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# Timestep Number-of-bins
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# Bin r Count value1 value2 ...
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</PRE>
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<P>In the first line, ID and name are replaced with the fix-ID and group
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name. The second line describes the two values that are printed at
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the first of each section of output. In the third line the values are
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replaced with the appropriate fields from the fix ave/spatial command.
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The Coord2 and Coord3 entries in the third line only appear for 2d and
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3d bins respectively. For 1d bins, the word Coord1 is replaced by
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just Coord.
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</P>
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<HR>
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<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
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</P>
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<P>No information about this fix is written to <A HREF = "restart.html">binary restart
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files</A>. None of the <A HREF = "fix_modify.html">fix_modify</A> options
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are relevant to this fix.
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</P>
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<P>This fix computes a global array of values which can be accessed by
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various <A HREF = "Section_howto.html#howto_15">output commands</A>. The values can
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only be accessed on timesteps that are multiples of <I>Nfreq</I> since that
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is when averaging is performed. The global array has # of rows =
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Nbins and # of columns = 2+Nvalues. The first column contains the
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radius at the center of the shell. For units <I>reduced</I>, this is in
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reduced units, while for units <I>box</I> and <I>lattice</I> this is in box
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units. The next column has the count of atoms in that bin, and the
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remaining columns are the Nvalue quantities. When the array is
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accessed with an I that exceeds the current number of bins, than a 0.0
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is returned by the fix instead of an error. The array values
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calculated by this fix are "intensive", since they are already
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normalized by the count of atoms in each bin.
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</P>
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<P>No parameter of this fix can be used with the <I>start/stop</I> keywords of
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the <A HREF = "run.html">run</A> command. This fix is not invoked during <A HREF = "minimize.html">energy
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minimization</A>.
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</P>
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<P><B>Restrictions:</B>
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</P>
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<P>When the <I>ave</I> keyword is set to <I>running</I> or <I>window</I> then the number
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of bins must remain the same during the simulation, so that the
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appropriate averaging can be done. This will be the case if the
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simulation box size doesn't change or if the <I>units</I> keyword is set to
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<I>reduced</I>.
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</P>
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<P>This style is part of the USER-MISC package. It is only enabled if
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LAMMPS is build with that package. See the <A HREF = "Section_start.html#3">Making of
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LAMMPS</A> section for more info.
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</P>
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<P><B>Related commands:</B>
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</P>
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<P><A HREF = "compute.html">compute</A>, <A HREF = "fix_ave_atom.html">fix ave/atom</A>, <A HREF = "fix_ave_histo.html">fix
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ave/histo</A>, <A HREF = "fix_ave_time.html">fix ave/time</A>,
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<A HREF = "variable.html">variable</A>, <A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
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<A HREF = "fix_ave_spatial.html">fix ave/spatial</A>,
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</P>
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<P><B>Default:</B>
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</P>
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<P>The option defaults are norm = all, ave = one, units = lattice, no
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file output, and title 1,2,3 = strings as described above.
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</P>
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</HTML>
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