2007-02-21 08:18:41 +08:00
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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/spatial 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 Nevery Nrepeat Nfreq dim origin delta ... 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>dim, origin, delta can be repeated 1, 2, or 3 times for 1d, 2d, or 3d bins
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2010-10-27 23:48:03 +08:00
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<PRE> dim = <I>x</I> or <I>y</I> or <I>z</I>
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origin = <I>lower</I> or <I>center</I> or <I>upper</I> or coordinate value (distance units)
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delta = thickness of spatial bins in dim (distance units)
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</PRE>
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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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2010-11-30 02:38:04 +08:00
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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>norm</I> or <I>units</I> or <I>file</I> or <I>ave</I> or <I>overwrite</I> or <I>title1</I> or <I>title2</I> or <I>title3</I>
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2007-10-19 08:33:05 +08:00
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<PRE> <I>units</I> arg = <I>box</I> or <I>lattice</I> or <I>reduced</I>
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<I>norm</I> arg = <I>all</I> or <I>sample</I>
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<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>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 10000 1 10000 z lower 0.02 c_myCentro units reduced &
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title1 "My output values"
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fix 1 flow ave/spatial 100 10 1000 y 0.0 1.0 vx vz norm sample file vel.profile
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fix 1 flow ave/spatial 100 5 1000 z lower 1.0 y 0.0 2.5 density/mass ave running
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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 1d, 2d, or 3d bins 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
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atom 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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2007-02-21 08:18:41 +08:00
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</P>
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2009-12-15 09:21:23 +08:00
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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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2010-10-27 23:48:03 +08:00
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<P>The size and dimensionality of the bins (1d = layers or slabs, 2d =
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pencils, 3d = boxes) are determined by the <I>dim</I>, <I>origin</I>, and
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<I>delta</I> settings and how many times they are specified (1, 2, or 3).
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See details below.
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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 (easy to do for 2d or 3d bins) will incur an
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overhead in memory and computational cost (summing across processors),
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so be careful to use reasonable numbers of bins.
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</P>
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2008-01-03 03:25:15 +08:00
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<HR>
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2007-10-19 06:27:53 +08:00
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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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2010-11-23 23:13:14 +08:00
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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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2010-10-27 23:48:03 +08:00
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<P>Each per-atom property is also averaged over atoms in each bin. Bins
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can be 1d layers or slabs, 2d pencils, or 3d boxes. This depends on
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how many times (1, 2, or 3) the <I>dim</I>, <I>origin</I>, and <I>delta</I> settings
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are specified in the fix ave/spatial command. For 2d or 3d bins,
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there is no restriction on specifying dim = x before dim = y, or dim =
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y before dim = z. Bins in a particular <I>dim</I> have a bin size in that
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dimension given by <I>delta</I>. Every Nfreq steps, when averaging is
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being performed and the per-atom property is calculated for the first
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time, the number of bins and the bin sizes and boundaries are
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computed. Thus if the simulation box changes size during a
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simulation, the number of bins and their boundaries may also change.
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In each dimension, bins are defined relative to a specified <I>origin</I>,
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which may be the lower/upper edge of the simulation box (in <I>dim</I>) or
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its center point, or a specified coordinate value. Starting at the
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origin, sufficient bins are created in both directions to completely
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cover the box. On subsequent timesteps every atom is mapped to one of
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the bins. Atoms beyond the lowermost/uppermost bin in a dimension are
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counted in the first/last bin in that dimension.
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</P>
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<P>For orthogonal simulation boxes, the bins are also layers, pencils, or
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boxes aligned with the xyz coordinate axes. For triclinic
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(non-orthogonal) simulation boxes, the bins are so that they are
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parallel to the tilted faces of the simulation box. See <A HREF = "Section_howto.html#howto_12">this
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section</A> of the manual for a discussion of
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the geometry of triclinic boxes in LAMMPS. As described there, a
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tilted simulation box has edge vectors a,b,c. In that nomenclature,
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bins in the x dimension have faces with normals in the "b" cross "c"
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direction. Bins in y have faces normal to the "a" cross "c"
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direction. And bins in z have faces normal to the "a" cross "b"
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direction. Note that in order to define the size and position of
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these bins in an unambiguous fashion, the <I>units</I> option must be set
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to <I>reduced</I> when using a triclinic simulation box, as noted below.
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</P>
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<HR>
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2010-11-30 02:38:04 +08:00
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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 bind, 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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2010-08-06 22:54:35 +08:00
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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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</P>
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<P>If a value begins with "c_", a compute ID must follow which has been
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2009-12-10 05:20:59 +08:00
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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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2012-05-18 06:29:43 +08:00
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bracketed integer is appended, the Ith column of the per-atom array
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2009-12-05 05:04:00 +08:00
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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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2008-01-03 03:25:15 +08:00
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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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2009-12-10 05:20:59 +08:00
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previously defined in the input script. If no bracketed integer is
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2009-12-05 05:04:00 +08:00
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appended, the per-atom vector calculated by the fix is used. If a
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2009-12-10 05:20:59 +08:00
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bracketed integer is appended, the Ith column of the per-atom array
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2009-12-05 05:04:00 +08:00
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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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2008-01-03 03:25:15 +08:00
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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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2009-12-10 05:20:59 +08:00
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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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2007-10-19 06:27:53 +08:00
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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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</P>
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2007-02-21 08:49:36 +08:00
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<P>The <I>units</I> keyword determines the meaning of the distance units used
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for the bin size <I>delta</I> and for <I>origin</I> if it is a coordinate
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value. For orthogonal simulation boxes, any of the 3 options may be
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2007-10-19 06:27:53 +08:00
|
|
|
used. For non-orthogonal (triclinic) simulation boxes, only the
|
2007-06-27 05:47:46 +08:00
|
|
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<I>reduced</I> option 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
|
|
|
|
|
define the lattice spacing. A <I>reduced</I> value means normalized
|
|
|
|
|
unitless values between 0 and 1, which represent the lower and upper
|
|
|
|
|
faces of the simulation box respectively. Thus an <I>origin</I> value of
|
|
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0.5 means the center of the box in any dimension. A <I>delta</I> value of
|
2010-10-27 23:48:03 +08:00
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0.1 means 10 bins span the box in that dimension.
|
2007-06-27 05:47:46 +08:00
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</P>
|
2010-10-27 23:48:03 +08:00
|
|
|
<P>Consider a non-orthogonal box, with bins that are 1d layers or slabs
|
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in the x dimension. No matter how the box is tilted, an <I>origin</I> of
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0.0 means start layers at the lower "b" cross "c" plane of the
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simulation box and an <I>origin</I> of 1.0 means to start layers at the
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upper "b" cross "c" face of the box. A <I>delta</I> value of 0.1 means
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there will be 10 layers from 0.0 to 1.0, regardless of the current
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size or shape of the simulation box.
|
2007-02-21 08:49:36 +08:00
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</P>
|
2008-01-03 03:25:15 +08:00
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|
<P>The <I>norm</I> keyword affects how averaging is done for the output
|
2010-10-27 23:48:03 +08:00
|
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|
produced every <I>Nfreq</I> timesteps. For an <I>all</I> setting, a bin
|
2008-01-03 03:25:15 +08:00
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quantity is summed over all atoms in all <I>Nrepeat</I> samples, as is the
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2010-10-27 23:48:03 +08:00
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|
count of atoms in the bin. The printed value for the bin is
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2008-01-03 03:25:15 +08:00
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|
Total-quantity / Total-count. In other words it is an average over
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2007-10-19 06:27:53 +08:00
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the entire <I>Nfreq</I> timescale.
|
2007-02-21 08:49:36 +08:00
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</P>
|
2010-10-27 23:48:03 +08:00
|
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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
|
2007-02-21 08:49:36 +08:00
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computed, i.e. Sample-quantity / Sample-count. The printed value for
|
2010-10-27 23:48:03 +08:00
|
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the bin is the average of the <I>Nrepeat</I> "average sample values", In
|
2007-10-19 06:27:53 +08:00
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other words it is an average of an average.
|
2007-02-21 08:18:41 +08:00
|
|
|
</P>
|
2010-10-27 23:48:03 +08:00
|
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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
|
|
|
|
|
command or written to a file.
|
2007-10-19 06:27:53 +08:00
|
|
|
</P>
|
2010-10-27 23:48:03 +08:00
|
|
|
<P>If the <I>ave</I> setting is <I>one</I>, then the bin values produced on
|
2007-10-19 06:27:53 +08:00
|
|
|
timesteps that are multiples of <I>Nfreq</I> are independent of each other;
|
|
|
|
|
they are output as-is without further averaging.
|
|
|
|
|
</P>
|
2010-10-27 23:48:03 +08:00
|
|
|
<P>If the <I>ave</I> setting is <I>running</I>, then the bin values produced on
|
2007-10-19 06:27:53 +08:00
|
|
|
timesteps that are multiples of <I>Nfreq</I> are summed and averaged in a
|
2010-10-27 23:48:03 +08:00
|
|
|
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
|
|
|
|
|
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
|
2007-10-19 06:27:53 +08:00
|
|
|
re-specifying it.
|
|
|
|
|
</P>
|
2010-10-27 23:48:03 +08:00
|
|
|
<P>If the <I>ave</I> setting is <I>window</I>, then the bin values produced on
|
2007-10-19 06:27:53 +08:00
|
|
|
timesteps that are multiples of <I>Nfreq</I> are summed and averaged within
|
2010-10-27 23:48:03 +08:00
|
|
|
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.
|
2007-10-19 06:27:53 +08:00
|
|
|
</P>
|
2009-12-12 05:41:25 +08:00
|
|
|
<P>The <I>file</I> keyword allows a filename to be specified. Every <I>Nfreq</I>
|
2010-10-27 23:48:03 +08:00
|
|
|
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
|
2009-12-12 05:41:25 +08:00
|
|
|
<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>
|
2012-06-19 22:10:51 +08:00
|
|
|
<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>
|
2009-12-10 05:20:59 +08:00
|
|
|
<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
|
2009-12-12 05:41:25 +08:00
|
|
|
values for each of these, so they do not need to be specified.
|
|
|
|
|
</P>
|
|
|
|
|
<P>By default, these header lines are as follows:
|
2009-12-10 05:20:59 +08:00
|
|
|
</P>
|
|
|
|
|
<PRE># Spatial-averaged data for fix ID and group name
|
2010-10-27 23:48:03 +08:00
|
|
|
# Timestep Number-of-bins
|
|
|
|
|
# Bin Coord1 Coord2 Coord3 Count value1 value2 ...
|
2009-12-10 05:20:59 +08:00
|
|
|
</PRE>
|
|
|
|
|
<P>In the first line, ID and name are replaced with the fix-ID and group
|
2009-12-12 05:41:25 +08:00
|
|
|
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.
|
2010-10-27 23:48:03 +08:00
|
|
|
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.
|
2009-12-10 05:20:59 +08:00
|
|
|
</P>
|
2007-10-19 06:27:53 +08:00
|
|
|
<HR>
|
|
|
|
|
|
2007-10-11 06:28:11 +08:00
|
|
|
<P><B>Restart, fix_modify, output, run start/stop, minimize info:</B>
|
2007-06-26 08:03:39 +08:00
|
|
|
</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
|
2007-10-15 23:07:59 +08:00
|
|
|
are relevant to this fix.
|
|
|
|
|
</P>
|
2009-12-10 05:20:59 +08:00
|
|
|
<P>This fix computes a global array of values which can be accessed by
|
2011-08-26 01:01:01 +08:00
|
|
|
various <A HREF = "Section_howto.html#howto_15">output commands</A>. The values can
|
2007-10-15 23:07:59 +08:00
|
|
|
only be accessed on timesteps that are multiples of <I>Nfreq</I> since that
|
2009-12-15 09:21:23 +08:00
|
|
|
is when averaging is performed. The global array has # of rows =
|
2010-10-27 23:48:03 +08:00
|
|
|
Nbins and # of columns = Ndim+1+Nvalues, where Ndim = 1,2,3 for
|
|
|
|
|
1d,2d,3d bins. The first 1 or 2 or 3 columns have the bin coordinates
|
|
|
|
|
(center of the bin) in the appropriate dimensions, 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, since the number of bins can vary as a simulation runs,
|
|
|
|
|
depending on the simulation box size. 2d or 3d bins are ordered so
|
|
|
|
|
that the last dimension(s) vary fastest. The array values calculated
|
|
|
|
|
by this fix are "intensive", since they are already normalized by the
|
|
|
|
|
count of atoms in each bin.
|
2007-10-15 23:07:59 +08:00
|
|
|
</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>.
|
2007-06-26 08:03:39 +08:00
|
|
|
</P>
|
2007-10-19 08:33:05 +08:00
|
|
|
<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
|
2010-10-27 23:48:03 +08:00
|
|
|
of bins must remain the same during the simulation, so that the
|
2007-10-19 08:33:05 +08:00
|
|
|
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>.
|
2007-02-21 08:18:41 +08:00
|
|
|
</P>
|
|
|
|
|
<P><B>Related commands:</B>
|
|
|
|
|
</P>
|
2009-12-15 09:21:23 +08:00
|
|
|
<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>,
|
2010-08-18 05:58:29 +08:00
|
|
|
<A HREF = "variable.html">variable</A>, <A HREF = "fix_ave_correlate.html">fix ave/correlate</A>,
|
2007-02-21 08:18:41 +08:00
|
|
|
</P>
|
2007-02-21 08:49:36 +08:00
|
|
|
<P><B>Default:</B>
|
|
|
|
|
</P>
|
2007-10-19 06:27:53 +08:00
|
|
|
<P>The option defaults are units = lattice, norm = all, no file output,
|
2009-12-10 05:20:59 +08:00
|
|
|
and ave = one, title 1,2,3 = strings as described above.
|
2007-02-21 08:18:41 +08:00
|
|
|
</P>
|
|
|
|
|
</HTML>
|
