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458 lines
24 KiB
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<HTML>
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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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<HR>
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<H3>fix ave/chunk 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/chunk Nevery Nrepeat Nfreq chunkID 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/chunk = 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>chunkID = ID of <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command
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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, temp, 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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temp = temperature
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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>norm</I> or <I>ave</I> or <I>bias</I> or <I>adof</I> or <I>cdof</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>norm</I> arg = <I>all</I> or <I>sample</I> or <I>none</I> = how output on <I>Nfreq</I> steps is normalized
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all = output is sum of atoms across all <I>Nrepeat</I> samples, divided by atom count
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sample = output is sum of <I>Nrepeat</I> sample averages, divided by <I>Nrepeat</I>
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none = output is sum of <I>Nrepeat</I> sums, divided by <I>Nrepeat</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>bias</I> arg = bias-ID
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bias-ID = ID of a temperature compute that removes a velocity bias for temperature calculation
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<I>adof</I> value = dof_per_atom
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dof_per_atom = define this many degrees-of-freedom per atom for temperature calculation
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<I>cdof</I> value = dof_per_chunk
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dof_per_chunk = define this many degrees-of-freedom per chunk for temperature calculation
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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/chunk 10000 1 10000 binchunk c_myCentro title1 "My output values"
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fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
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fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
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fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
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</PRE>
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<P><B>IMPORTANT NOTE:</B>
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</P>
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<P>If you are trying to replace an older fix ave/spatial command with the
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newer, more flexible fix ave/chunk and <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> commands, you simply need to split
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the fix ave/spatial arguments across the two new commands. For
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example, this command:
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</P>
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<PRE>fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
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</PRE>
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<P>could be replaced by:
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</P>
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<PRE>compute cc1 flow chunk/atom bin/1d y 0.0 1.0
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fix 1 flow ave/chunk 100 10 1000 cc1 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, sum
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the values over the atoms in each chunk at each timestep, then average
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the per-chunk values over longer timescales. The resulting chunk
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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>In LAMMPS, chunks are collections of atoms defined by a <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> command, which assigns each atom
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to a single chunk (or no chunk). The ID for this command is specified
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as chunkID. For example, a single chunk could be the atoms in a
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molecule or atoms in a spatial bin. See the <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> doc page and "<A HREF = "Section_howto.html#howto_23">Section_howto
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23</A> for details of how chunks can be
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defined and examples of how they can be used to measure properties of
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a system.
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</P>
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<P>Note that only atoms in the specified group contribute to the summing
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and averaging calculations. The <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> command defines its own group as
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well as an optional region. Atoms will have a chunk ID = 0, meaning
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they belong to no chunk, if they are not in that group or region.
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Thus you can specify the "all" group for this command if you simply
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want to use the chunk definitions provided by chunkID.
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</P>
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<P>Each specified per-atom value can be an atom attribute (position,
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velocity, force component), a mass or number density, or the result of
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a <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. Note that the <A HREF = "compute_property_atom.html">compute
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property/atom</A> command provides access to
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any attribute defined and stored by atoms. If you wish to
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time-average global quantities from a compute, fix, or variable, then
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see the <A HREF = "fix_ave_time.html">fix 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 summed 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>IMPORTANT NOTE: This fix works by creating an array of size <I>Nchunk</I>
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by Nvalues on each processor. <I>Nchunk</I> is the number of chunks which
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is defined by the <A HREF = "doc/compute_chunk_atom.html">compute chunk/atom</A>
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command. Nvalues is the number of input values specified. Each
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processor loops over its atoms, tallying its values to the appropriate
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chunk. Then the entire array is summed across all processors. This
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means that using a large number of chunks will incur an overhead in
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memory and computational cost (summing across processors), so be
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careful to define a reasonable number of chunks.
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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 accessed and contribute to the
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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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<P>Each input value can also be averaged over the atoms in each chunk.
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The way the averaging is done across the <I>Nrepeat</I> timesteps to
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produce output on the <I>Nfreq</I> timesteps, and across multiple <I>Nfreq</I>
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outputs, is determined by the <I>norm</I> and <I>ave</I> keyword settings, as
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discussed below.
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</P>
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<P>IMPORTANT NOTE: To perform per-chunk averaging within a <I>Nfreq</I> time
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window, the number of chunks <I>Nchunk</I> defined by the <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> command must remain constant. If
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the <I>ave</I> keyword is set to <I>running</I> or <I>window</I> then <I>Nchunk</I> must
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remain constant for the duration of the simulation. This fix forces
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the chunk/atom compute specified by chunkID to hold <I>Nchunk</I> constant
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for the appropriate time windows, by not allowing it to re-calcualte
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<I>Nchunk</I>, which can also affect how it assigns chunk IDs to atoms.
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More details are given on the <A HREF = "compute_chunk_atom.html">compute
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chunk/atom</A> doc page.
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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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As noted above, any other atom attributes can be used as input values
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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 for
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each chunk, i.e. number/volume. The <I>density/mass</I> value means the
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mass density is computed for each chunk, i.e. total-mass/volume. The
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output values are in units of 1/volume or density (mass/volume). See
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the <A HREF = "units.html">units</A> command doc page for the definition of density
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for each choice of units, e.g. gram/cm^3. If the chunks defined by
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the <A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command are spatial
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bins, the volume is the bin volume. Otherwise it is the volume of the
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entire simulation box.
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</P>
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<P>The <I>temp</I> value means the temperature is computed for each chunk, by
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the formula KE = DOF/2 k T, where KE = total kinetic energy of the
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chunk of atoms (sum of 1/2 m v^2), DOF = the total number of degrees
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of freedom for all atoms in the chunk, k = Boltzmann constant, and T =
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temperature.
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</P>
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<P>The DOF is calculated as N*adof + cdof, where N = number of atoms in
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the chunk, adof = degrees of freedom per atom, and cdof = degrees of
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freedom per chunk. By default adof = 2 or 3 = dimensionality of
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system, as set via the <A HREF = "dimension.html">dimension</A> command, and cdof =
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0.0. This gives the usual formula for temperature.
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</P>
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<P>Note that currently this temperature only includes translational
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degrees of freedom for each atom. No rotational degrees of freedom
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are included for finite-size particles. Also no degrees of freedom
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are subtracted for any velocity bias or constraints that are applied,
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such as <A HREF = "compute_temp_partial.html">compute temp/partial</A>, or <A HREF = "fix_shake.html">fix
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shake</A> or <A HREF = "fix_rigid.html">fix rigid</A>. This is because
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those degrees of freedom (e.g. a constrained bond) could apply to sets
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of atoms that are both included and excluded from a specific chunk,
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and hence the concept is somewhat ill-defined. In some cases, you can
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use the <I>adof</I> and <I>cdof</I> keywords to adjust the calculated degress of
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freedom appropriately, as explained below.
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</P>
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<P>Also note that a bias can be subtracted from atom velocities before
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they are used in the above formula for KE, by using the <I>bias</I>
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keyword. This allows, for example, a thermal temperature to be
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computed after removal of a flow velocity profile.
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</P>
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<P>Note that the per-chunk temperature calculated by this fix and the
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<A HREF = "compute_temp_chunk.html">compute temp/chunk</A> command can be different.
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The compute calculates the temperature for each chunk for a single
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snapshot. This fix can do that but can also time average those values
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over many snapshots, or it can compute a temperature as if the atoms
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in the chunk on different timesteps were collected together as one set
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of atoms to calculate their temperature. The compute allows the
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center-of-mass velocity of each chunk to be subtracted before
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calculating the temperature; this fix does not.
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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 average within chunks.
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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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and its outputs.
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</P>
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<P>The <I>norm</I> keyword affects how averaging is done for the per-chunk
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values that are output every <I>Nfreq</I> timesteps.
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</P>
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<P>It the <I>norm</I> setting is <I>all</I>, which is the default, a chunk value is
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summed over all atoms in all <I>Nrepeat</I> samples, as is the count of
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atoms in the chunk. The averaged output value for the chunk on the
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<I>Nfreq</I> timesteps is Total-sum / Total-count. In other words it is an
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average over atoms across the entire <I>Nfreq</I> timescale.
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</P>
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<P>If the <I>norm</I> setting is <I>sample</I>, the chunk value is summed over atoms
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for each sample, as is the count, and an "average sample value" is
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computed for each sample, i.e. Sample-sum / Sample-count. The outuput
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value for the chunk on the <I>Nfreq</I> timesteps is the average of the
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<I>Nrepeat</I> "average sample values", i.e. the sum of <I>Nrepeat</I> "average
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sample values" divided by <I>Nrepeat</I>. In other words it is an average
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of an average.
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</P>
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<P>If the <I>norm</I> setting is <I>none</I>, a similar computation as for the
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<I>sample</I> seting is done, except the individual "average sample values"
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are "summed sample values". A summed sample value is simply the chunk
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value summed over atoms in the sample, without dividing by the number
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of atoms in the sample. The outuput value for the chunk on the
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<I>Nfreq</I> timesteps is the average of the <I>Nrepeat</I> "summed sample
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values", i.e. the sum of <I>Nrepeat</I> "summed sample values" divided by
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<I>Nrepeat</I>.
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</P>
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<P>The <I>ave</I> keyword determines how the per-chunk values produced every
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<I>Nfreq</I> steps are averaged with 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>, which is the default, then the chunk
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values produced on timesteps that are multiples of <I>Nfreq</I> are
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independent of each other; they are output as-is without further
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averaging.
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</P>
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<P>If the <I>ave</I> setting is <I>running</I>, then the chunk 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 chunk value is thus
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the average of the chunk value produced on that timestep with all
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preceding values for the same chunk. 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 chunk 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
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chunk are used to produce the output. E.g. if M = 3 and Nfreq = 1000,
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then the output on step 10000 will be the average of the individual
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chunk values on steps 8000,9000,10000. Outputs on early steps will
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average over less than M values if they are not available.
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</P>
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<P>The <I>bias</I> keyword specifies the ID of a temperature compute that
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removes a "bias" velocity from each atom, specified as <I>bias-ID</I>. It
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is only used when the <I>temp</I> value is calculated, to compute the
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thermal temperature of each chunk after the translational kinetic
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energy components have been altered in a prescribed way, e.g. to
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remove a flow velocity profile. See the doc pages for individual
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computes that calculate a temperature to see which ones implement a
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bias.
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</P>
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<P>The <I>adof</I> and <I>cdof</I> keywords define the values used in the degree of
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freedom (DOF) formula described above for for temperature calculation
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for each chunk. They are only used when the <I>temp</I> value is
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calculated. They can be used to calculate a more appropriate
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temperature for some kinds of chunks. Here are 3 examples:
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</P>
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<P>If spatially binned chunks contain some number of water molecules and
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<A HREF = "fix_shake.html">fix shake</A> is used to make each molecule rigid, then
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you could calculate a temperature with 6 degrees of freedom (DOF) (3
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translational, 3 rotational) per molecule by setting <I>adof</I> to 2.0.
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</P>
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<P>If <A HREF = "compute_temp_partial.html">compute temp/partial</A> is used with the
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<I>bias</I> keyword to only allow the x component of velocity to contribute
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to the temperature, then <I>adof</I> = 1.0 would be appropriate.
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</P>
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<P>If each chunk consists of a large molecule, with some number of its
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bonds constrained by <A HREF = "fix_shake.html">fix shake</A> or the entire molecule
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by <A HREF = "fix_rigid.html">fix rigid/small</A>, <I>adof</I> = 0.0 and <I>cdof</I> could be
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set to the remaining degrees of freedom for the entire molecule
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(entire chunk in this case), e.g. 6 for 3d, or 3 for 2d, for a rigid
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molecule.
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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 chunk info will be written to a text file in
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the following format. A line with the timestep and number of chunks
|
|
is written. Then one line per chunk is written, containing the chunk
|
|
ID (1-Nchunk), an optional original ID value, optional coordinate
|
|
values for chunks that represent spatial bins, the number of atoms in
|
|
the chunk, and one or more calculated values. More explanation of the
|
|
optional values is given below. The number of values in each line
|
|
corresponds to the number of values specified in the fix ave/chunk
|
|
command. The number of atoms and the value(s) are summed or average
|
|
quantities, as explained above.
|
|
</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># Chunk-averaged data for fix ID and group name
|
|
# Timestep Number-of-chunks
|
|
# Chunk (OrigID) (Coord1) (Coord2) (Coord3) Ncount 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 value names, e.g. fx or c_myCompute<B>2</B>.
|
|
</P>
|
|
<P>The words in parenthesis only appear with corresponding columns if the
|
|
chunk style specified for the <A HREF = "compute_chunk_atom.html">compute
|
|
chunk/atom</A> command supports them. The OrigID
|
|
column is only used if the <I>compress</I> keyword was set to <I>yes</I> for the
|
|
<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command. This means that
|
|
the original chunk IDs (e.g. molecule IDs) will have been compressed
|
|
to remove chunk IDs with no atoms assigned to them. Thus a compresed
|
|
chunk ID of 3 may correspond to an original chunk ID or molecule ID of
|
|
415. The OrigID column will list 415 for the 3rd chunk.
|
|
</P>
|
|
<P>The CoordN columns only appear if a <I>binning</I> style was used in the
|
|
<A HREF = "compute_chunk_atom.html">compute chunk/atom</A> command. For <I>bin/1d</I>,
|
|
<I>bin/2d</I>, and <I>bin/3d</I> styles the column values are the center point
|
|
of the bin in the corresponding dimension. Just Coord1 is used for
|
|
<I>bin/1d</I>, Coord2 is added for <I>bin/2d</I>, Coord3 is added for <I>bin/3d</I>.
|
|
</P>
|
|
<P>Note that if the value of the <I>units</I> keyword used in the <A HREF = "compute_chunk_atom.html">compute
|
|
chunk/atom command</A> is <I>box</I> or <I>lattice</I>, the
|
|
coordinate values will be in distance <A HREF = "units.html">units</A>. If the
|
|
value of the <I>units</I> keyword is <I>reduced</I>, the coordinate values will
|
|
be in unitless reduced units (0-1).
|
|
</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 =
|
|
the number of chunks <I>Nchunk</I> as calculated by the specified <A HREF = "compute_chunk_atom.html">compute
|
|
chunk/atom</A> command. The # of columns =
|
|
M+1+Nvalues, where M = 1 to 4, depending on whether the optional
|
|
columns for OrigID and CoordN are used, as explained above.
|
|
Following the optional columns, the next column contains the count of
|
|
atoms in the chunk, and the remaining columns are the Nvalue
|
|
quantities. When the array is accessed with a row I that exceeds the
|
|
current number of chunks, than a 0.0 is returned by the fix instead of
|
|
an error, since the number of chunks can vary as a simulation runs
|
|
depending on how that value is computed by the compute chunk/atom
|
|
command.
|
|
</P>
|
|
<P>The array values calculated by this fix are treated as "intensive",
|
|
since they are typically already normalized by the count of atoms in
|
|
each chunk.
|
|
</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> none
|
|
</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>
|
|
</P>
|
|
<P><B>Default:</B>
|
|
</P>
|
|
<P>The option defaults are norm = all, ave = one, bias = none, no file output, and
|
|
title 1,2,3 = strings as described above.
|
|
</P>
|
|
</HTML>
|